uboot: (firmwareOdroidC2/C4) don't invoke patch tool, use patches = [] instead

https://github.com/NixOS/nixpkgs/blob/master/pkgs/stdenv/generic/setup.sh#L948
this can do it nicely.

Signed-off-by: Anton Arapov <anton@deadbeef.mx>

pkgs/applications/science/math/sage/README.md

@@ -0,0 +1,78 @@
+# Sage on nixos
+
+Sage is a pretty complex package that depends on many other complex packages and patches some of those. As a result, the sage nix package is also quite complex.
+
+Don't feel discouraged to fix, simplify or improve things though. The individual files have comments explaining their purpose. The most importent ones are `default.nix` linking everything together, `sage-src.nix` adding patches and `sagelib.nix` building the actual sage package.
+
+## The sage build is broken
+
+First you should find out which change to nixpkgs is at fault (if you don't already know). You can use `git-bisect` for that (see the manpage).
+
+If the build broke as a result of a package update, try those solutions in order:
+
+- search the [sage trac](https://trac.sagemath.org/) for keywords like "Upgrade <package>". Maybe somebody has already proposed a patch that fixes the issue. You can then add a `fetchpatch` to `sage-src.nix`.
+
+- check if [gentoo](https://github.com/cschwan/sage-on-gentoo/tree/master/sci-mathematics/sage), [debian](https://salsa.debian.org/science-team/sagemath/tree/master/debian) or [arch linux](https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath) already solved the problem. You can then again add a `fetchpatch` to `sage-src.nix`. If applicable you should also [propose the patch upstream](#proposing-a-sage-patch).
+
+- fix the problem yourself. First clone the sagemath source and then check out the sage version you want to patch:
+
+```
+[user@localhost ~]$ git clone https://github.com/sagemath/sage.git
+[user@localhost ~]$ cd sage
+[user@localhost sage]$ git checkout 8.2 # substitute the relevant version here
+```
+
+Then make the needed changes and generate a patch with `git diff`:
+
+```
+[user@localhost ~]$ <make changes>
+[user@localhost ~]$ git diff -u > /path/to/nixpkgs/pkgs/applications/science/math/sage/patches/name-of-patch.patch
+```
+
+Now just add the patch to `sage-src.nix` and test your changes. If they fix the problem, [propose them upstream](#proposing-a-sage-patch) and add a link to the trac ticket.
+
+- pin the package version in `default.nix` and add a note that explains why that is necessary.
+
+
+## Proposing a sage patch
+
+You can [login the sage trac using GitHub](https://trac.sagemath.org/login). Your username will then be `gh-<your-github-name>`. The only other way is to request a trac account via email. After that refer to [git the hard way](http://doc.sagemath.org/html/en/developer/manual_git.html#chapter-manual-git) in the sage documentation. The "easy way" requires a non-GitHub account (requested via email) and a special tool. The "hard way" is really not all that hard if you're a bit familiar with git.
+
+Here's the gist, assuming you want to use ssh key authentication. First, [add your public ssh key](https://trac.sagemath.org/prefs/sshkeys). Then:
+
+```
+[user@localhost ~]$ git clone https://github.com/sagemath/sage.git
+[user@localhost ~]$ cd sage
+[user@localhost sage]$ git remote add trac git@trac.sagemath.org:sage.git -t master
+[user@localhost sage]$ git checkout -b u/gh-<your-github-username>/<your-branch-name> develop
+[user@localhost sage]$ <make changes>
+[user@localhost sage]$ git add .
+[user@localhost sage]$ git commit
+[user@localhost sage]$ git show # review your changes
+[user@localhost sage]$ git push --set-upstream trac u/gh-<your-github-username>/<your-branch-name>
+```
+
+You now created a branch on the trac server (you *must* follow the naming scheme as you only have push access to branches with the `u/gh-<your-github-username>/` prefix).
+Now you can [create a new trac ticket](https://trac.sagemath.org/newticket).
+- Write a description of the change
+- set the type and component as appropriate
+- write your real name in the "Authors" field
+- write `u/gh-<your-github-username>/<your-branch-name>` in the "Branch" field
+- click "Create ticket"
+- click "Modify" on the top right of your ticket (for some reason you can only change the ticket status after you have created it)
+- set the ticket status from `new` to `needs_review`
+- click "Save changes"
+
+Refer to sages [Developer's Guide](http://doc.sagemath.org/html/en/developer/index.html) for further details.
+
+## I want to update sage
+
+You'll need to change the `version` field in `sage-src.nix`. Afterwards just try to build and let nix tell you which patches no longer apply (hopefully because they were adopted upstream). Remove those.
+
+Hopefully the build will succeed now. If it doesn't and the problem is obvious, fix it as described in [The sage build is broken](#the-sage-build-is-broken).
+If the problem is not obvious, you can try to first update sage to an intermediate version (remember that you can also set the `version` field to any git revision of sage) and locate the sage commit that introduced the issue. You can even use `git-bisect` for that (it will only be a bit tricky to keep track of which patches to apply). Hopefully after that the issue will be obvious.
+
+## Well, that didn't help!
+
+If you couldn't fix the problem, create a GitHub issue on the nixpkgs repo and ping @timokau (or whoever is listed in the `maintainers` list of the sage package).
+Describe what you did and why it didn't work. Afterwards it would be great if you help the next guy out and improve this documentation!

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

@@ -0,0 +1,177 @@
+{ pkgs
+, withDoc ? false
+, requireSageTests ? true
+, extraPythonPackages ? ps: []
+}:
+
+# Here sage and its dependencies are put together. Some dependencies may be pinned
+# as a last resort. Patching sage for compatibility with newer dependency versions
+# is always preferred, see `sage-src.nix` for that.
+
+let
+  inherit (pkgs) symlinkJoin callPackage nodePackages;
+
+  python3 = pkgs.python3.override {
+    packageOverrides = self: super: {
+      # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
+      sagelib = self.callPackage ./sagelib.nix {
+        inherit flint arb;
+        inherit sage-src env-locations singular;
+        inherit (maxima) lisp-compiler;
+        linbox = pkgs.linbox.override { withSage = true; };
+        pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
+      };
+
+      sage-docbuild = self.callPackage ./python-modules/sage-docbuild.nix {
+        inherit sage-src;
+      };
+
+      sage-setup = self.callPackage ./python-modules/sage-setup.nix {
+        inherit sage-src;
+      };
+    };
+  };
+
+  jupyter-kernel-definition = {
+    displayName = "SageMath ${sage-src.version}";
+    argv = [
+      "${sage-with-env}/bin/sage" # FIXME which sage
+      "--python"
+      "-m"
+      "sage.repl.ipython_kernel"
+      "-f"
+      "{connection_file}"
+    ];
+    language = "sagemath";
+    # just one 16x16 logo is available
+    logo32 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png";
+    logo64 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png";
+  };
+
+  jupyter-kernel-specs = pkgs.jupyter-kernel.create {
+    definitions = pkgs.jupyter-kernel.default // {
+      sagemath = jupyter-kernel-definition;
+    };
+  };
+
+  three = callPackage ./threejs-sage.nix { };
+
+  # 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;
+    inherit singular maxima;
+    inherit three;
+    cysignals = python3.pkgs.cysignals;
+    mathjax = nodePackages.mathjax;
+  };
+
+  # The shell file that gets sourced on every sage start. Will also source
+  # the env-locations file.
+  sage-env = callPackage ./sage-env.nix {
+    sagelib = python3.pkgs.sagelib;
+    sage-docbuild = python3.pkgs.sage-docbuild;
+    inherit env-locations;
+    inherit python3 singular palp flint pythonEnv maxima;
+    pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
+  };
+
+  # The documentation for sage, building it takes a lot of ram.
+  sagedoc = callPackage ./sagedoc.nix {
+    inherit sage-with-env jupyter-kernel-specs;
+  };
+
+  # 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 python3 pythonEnv;
+    inherit sage-env;
+    inherit singular maxima;
+    inherit three;
+    pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
+  };
+
+  # Doesn't actually build anything, just runs sages testsuite. This is a
+  # separate derivation to make it possible to re-run the tests without
+  # rebuilding sagelib (which takes ~30 minutes).
+  # Running the tests should take something in the order of 1h.
+  sage-tests = callPackage ./sage-tests.nix {
+    inherit sage-with-env;
+  };
+
+  sage-src = callPackage ./sage-src.nix {};
+
+  pythonRuntimeDeps = with python3.pkgs; [
+    sagelib
+    sage-docbuild
+    cvxopt
+    networkx
+    service-identity
+    psutil
+    sympy
+    fpylll
+    matplotlib
+    tkinter # optional, as a matplotlib backend (use with `%matplotlib tk`)
+    scipy
+    ipywidgets
+    rpy2
+    sphinx
+    pillow
+  ] ++ extraPythonPackages python3.pkgs;
+
+  pythonEnv = python3.buildEnv.override {
+    extraLibs = pythonRuntimeDeps;
+    ignoreCollisions = true;
+  } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
+
+  arb = pkgs.arb.override { inherit flint; };
+
+  singular = pkgs.singular.override { inherit flint; };
+
+  maxima = pkgs.maxima.override {
+    lisp-compiler = 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;
+    };
+  };
+
+  # With openblas (64 bit), the tests fail the same way as when sage is build with
+  # openblas instead of openblasCompat. Apparently other packages somehow use flints
+  # blas when it is available. Alternative would be to override flint to use
+  # openblasCompat.
+  flint = pkgs.flint.override { withBlas = false; };
+
+  # Multiple palp dimensions need to be available and sage expects them all to be
+  # in the same folder.
+  palp = symlinkJoin {
+    name = "palp-${pkgs.palp.version}";
+    paths = [
+      (pkgs.palp.override { dimensions = 4; doSymlink = false; })
+      (pkgs.palp.override { dimensions = 5; doSymlink = false; })
+      (pkgs.palp.override { dimensions = 6; doSymlink = true; })
+      (pkgs.palp.override { dimensions = 11; doSymlink = false; })
+    ];
+  };
+
+  # Sage expects those in the same directory.
+  pari_data = symlinkJoin {
+    name = "pari_data";
+    paths = with pkgs; [
+      pari-galdata
+      pari-seadata-small
+    ];
+  };
+in
+# A wrapper around sage that makes sure sage finds its docs (if they were build).
+callPackage ./sage.nix {
+  inherit sage-tests sage-with-env sagedoc jupyter-kernel-definition jupyter-kernel-specs;
+  inherit withDoc requireSageTests;
+}

pkgs/applications/science/math/sage/dist-tests.nix

@@ -0,0 +1,17 @@
+# Lists past failures and files associated with it. The intention is to build
+# up a subset of a testsuite that catches 95% of failures that are relevant for
+# distributions while only taking ~5m to run. This in turn makes it more
+# reasonable to re-test sage on dependency changes and makes it easier for
+# users to override the sage derivation.
+# This is an experiment for now. If it turns out that there really is a small
+# subset of files responsible for the vast majority of packaging tests, we can
+# think about moving this upstream.
+[
+	"src/sage/env.py" # [1]
+	"src/sage/misc/persist.pyx" # [1]
+	"src/sage/misc/inline_fortran.py" # [1]
+	"src/sage/repl/ipython_extension.py" # [1]
+]
+
+# Numbered list of past failures to annotate files with
+# [1] PYTHONPATH related issue https://github.com/NixOS/nixpkgs/commit/ec7f569211091282410050e89e68832d4fe60528

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

@@ -0,0 +1,48 @@
+{ writeTextFile
+, pari_data
+, pari
+, singular
+, maxima
+, conway_polynomials
+, graphs
+, elliptic_curves
+, polytopes_db
+, gap
+, combinatorial_designs
+, jmol
+, mathjax
+, three
+, cysignals
+}:
+
+# A bash script setting various environment variables to tell sage where
+# the files its looking fore are located. Also see `sage-env`.
+writeTextFile rec {
+  name = "sage-env-locations";
+  destination = "/${name}";
+  text = ''
+    export GP_DATA_DIR="${pari_data}/share/pari"
+    export PARI_DATA_DIR="${pari_data}"
+    export GPHELP="${pari}/bin/gphelp"
+    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}/lib/maxima/${maxima.version}/binary-ecl/maxima.fas'
+    export MAXIMA_PREFIX="${maxima}"
+    export CONWAY_POLYNOMIALS_DATA_DIR='${conway_polynomials}/share/conway_polynomials'
+    export GRAPHS_DATA_DIR='${graphs}/share/graphs'
+    export ELLCURVE_DATA_DIR='${elliptic_curves}/share/ellcurves'
+    export POLYTOPE_DATA_DIR='${polytopes_db}/share/reflexive_polytopes'
+    export GAP_ROOT_DIR='${gap}/share/gap/build-dir'
+    export ECLDIR='${maxima.lisp-compiler}/lib/${maxima.lisp-compiler.pname}-${maxima.lisp-compiler.version}/'
+    export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs"
+    export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona"
+    export JMOL_DIR="${jmol}/share/jmol" # point to the directory that contains JmolData.jar
+    export JSMOL_DIR="${jmol}/share/jsmol"
+    export MATHJAX_DIR="${mathjax}/lib/node_modules/mathjax"
+    export THREEJS_DIR="${three}/lib/node_modules/three"
+    export SAGE_INCLUDE_DIRECTORIES="${cysignals}/${cysignals.pythonModule.sitePackages}"
+  '';
+}

pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch

@@ -0,0 +1,19 @@
+diff --git a/src/sage/repl/configuration.py b/src/sage/repl/configuration.py
+index 67d7d2accf..18279581e2 100644
+--- a/src/sage/repl/configuration.py
++++ b/src/sage/repl/configuration.py
+@@ -9,10 +9,11 @@ the IPython simple prompt is being used::
+     sage: cmd = 'print([sys.stdin.isatty(), sys.stdout.isatty()])'
+     sage: import pexpect
+     sage: output = pexpect.run(
+-    ....:     'bash -c \'echo "{0}" | sage\''.format(cmd),
++    ....:     'bash -c \'export SAGE_BANNER=no; echo "{0}" | sage\''.format(cmd),
+     ....: ).decode('utf-8', 'surrogateescape')
+-    sage: 'sage: [False, True]' in output
+-    True
++    sage: print(output)
++    sage...[False, True]
++    ...
+ """
+ 
+ #*****************************************************************************

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

@@ -0,0 +1,87 @@
+diff --git a/src/sage/env.py b/src/sage/env.py
+index c4953cfa65..47b880f9ad 100644
+--- a/src/sage/env.py
++++ b/src/sage/env.py
+@@ -244,81 +244,8 @@ os.environ['MPMATH_SAGE'] = '1'
+ SAGE_BANNER = var("SAGE_BANNER", "")
+ SAGE_IMPORTALL = var("SAGE_IMPORTALL", "yes")
+ 
+-
+-def _get_shared_lib_path(*libnames: str) -> Optional[str]:
+-    """
+-    Return the full path to a shared library file installed in
+-    ``$SAGE_LOCAL/lib`` or the directories associated with the
+-    Python sysconfig.
+-
+-    This can also be passed more than one library name (e.g. for cases where
+-    some library may have multiple names depending on the platform) in which
+-    case the first one found is returned.
+-
+-    This supports most *NIX variants (in which ``lib<libname>.so`` is found
+-    under ``$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>/``).
+-
+-    This returns ``None`` if no matching library file could be found.
+-
+-    EXAMPLES::
+-
+-        sage: from sage.env import _get_shared_lib_path
+-        sage: "gap" in _get_shared_lib_path("gap")
+-        True
+-        sage: _get_shared_lib_path("an_absurd_lib") is None
+-        True
+-
+-    """
+-
+-    for libname in libnames:
+-        search_directories: List[Path] = []
+-        patterns: List[str] = []
+-        if sys.platform == 'cygwin':
+-            # Later down we take the first matching DLL found, so search
+-            # SAGE_LOCAL first so that it takes precedence
+-            if SAGE_LOCAL:
+-                search_directories.append(Path(SAGE_LOCAL) / 'bin')
+-            search_directories.append(Path(sysconfig.get_config_var('BINDIR')))
+-            # Note: The following is not very robust, since if there are multible
+-            # 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
+-            patterns = [f'cyg{libname}.dll', f'cyg{libname}-*.dll']
+-        else:
+-            if sys.platform == 'darwin':
+-                ext = 'dylib'
+-            else:
+-                ext = 'so'
+-
+-            if SAGE_LOCAL:
+-                search_directories.append(Path(SAGE_LOCAL) / 'lib')
+-            libdir = sysconfig.get_config_var('LIBDIR')
+-            if libdir is not None:
+-                libdir = Path(libdir)
+-                search_directories.append(libdir)
+-
+-                multiarchlib = sysconfig.get_config_var('MULTIARCH')
+-                if multiarchlib is not None:
+-                    search_directories.append(libdir / multiarchlib),
+-
+-            patterns = [f'lib{libname}.{ext}']
+-
+-        for directory in search_directories:
+-            for pattern in patterns:
+-                path = next(directory.glob(pattern), None)
+-                if path is not None:
+-                    return str(path.resolve())
+-
+-    # Just return None if no files were found
+-    return None
+-
+ # locate libgap shared object
+-GAP_SO = var("GAP_SO", _get_shared_lib_path("gap", ""))
++GAP_SO = var("GAP_SO", '/default')
+ 
+ # post process
+ if DOT_SAGE is not None and ' ' in DOT_SAGE:

pkgs/applications/science/math/sage/patches/docutils-0.18.1-deprecation.patch

@@ -0,0 +1,13 @@
+diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py
+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 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...'
+ 
+         In the 'text' version, double colons have been replaced with

pkgs/applications/science/math/sage/patches/fix-ecl-race.patch

@@ -0,0 +1,19 @@
+diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
+index 02e18e67e7..2ebf6eb35f 100644
+--- a/src/sage/doctest/forker.py
++++ b/src/sage/doctest/forker.py
+@@ -1075,6 +1075,14 @@ class SageDocTestRunner(doctest.DocTestRunner, object):
+             sage: set(ex2.predecessors) == set([ex0,ex1])
+             True
+         """
++
++        # Fix ECL dir race conditions by using a separate dir for each process
++        # (https://trac.sagemath.org/ticket/26968)
++        os.environ['MAXIMA_USERDIR'] = "{}/sage-maxima-{}".format(
++            tempfile.gettempdir(),
++            os.getpid()
++        )
++
+         if isinstance(globs, RecordingDict):
+             globs.start()
+         example.sequence_number = len(self.history)

pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch

@@ -0,0 +1,58 @@
+diff --git a/src/sage/libs/linbox/conversion.pxd b/src/sage/libs/linbox/conversion.pxd
+index 7794c9edc3..1753277b1f 100644
+--- a/src/sage/libs/linbox/conversion.pxd
++++ b/src/sage/libs/linbox/conversion.pxd
+@@ -177,9 +177,8 @@ cdef inline Vector_integer_dense new_sage_vector_integer_dense(P, DenseVector_in
+     - v -- linbox vector
+     """
+     cdef Vector_integer_dense res = P()
+-    cdef cppvector[Integer] * vec = &v.refRep()
+     cdef size_t i
+     for i in range(<size_t> res._degree):
+-        mpz_set(res._entries[i], vec[0][i].get_mpz_const())
++        mpz_set(res._entries[i], v.getEntry(i).get_mpz_const())
+ 
+     return res
+diff --git a/src/sage/libs/linbox/linbox.pxd b/src/sage/libs/linbox/linbox.pxd
+index 9112d151f8..dcc482960c 100644
+--- a/src/sage/libs/linbox/linbox.pxd
++++ b/src/sage/libs/linbox/linbox.pxd
+@@ -32,7 +32,7 @@ cdef extern from "linbox/matrix/dense-matrix.h":
+         ctypedef Modular_double Field
+         ctypedef double Element
+         DenseMatrix_Modular_double(Field F, size_t m, size_t n)
+-        DenseMatrix_Modular_double(Field F, Element*, size_t m, size_t n)
++        DenseMatrix_Modular_double(Field F, size_t m, size_t n, Element*)
+         void setEntry(size_t i, size_t j, Element& a)
+         Element &getEntry(size_t i, size_t j)
+ 
+@@ -42,7 +42,7 @@ cdef extern from "linbox/matrix/dense-matrix.h":
+         ctypedef Modular_float Field
+         ctypedef float Element
+         DenseMatrix_Modular_float(Field F, size_t m, size_t n)
+-        DenseMatrix_Modular_float(Field F, Element*, size_t m, size_t n)
++        DenseMatrix_Modular_float(Field F, size_t m, size_t n, Element*)
+         void setEntry(size_t i, size_t j, Element& a)
+         Element &getEntry(size_t i, size_t j)
+ 
+@@ -101,7 +101,6 @@ cdef extern from "linbox/vector/vector.h":
+         DenseVector_integer (Field &F)
+         DenseVector_integer (Field &F, long& m)
+         DenseVector_integer (Field &F, cppvector[Integer]&)
+-        cppvector[Element]& refRep()
+         size_t size()
+         void resize(size_t)
+         void resize(size_t n, const Element&)
+diff --git a/src/sage/matrix/matrix_modn_dense_template.pxi b/src/sage/matrix/matrix_modn_dense_template.pxi
+index 010365d76f..3d60726ff9 100644
+--- a/src/sage/matrix/matrix_modn_dense_template.pxi
++++ b/src/sage/matrix/matrix_modn_dense_template.pxi
+@@ -219,7 +219,7 @@ cdef inline linbox_echelonize_efd(celement modulus, celement* entries, Py_ssize_
+         return 0,[]
+ 
+     cdef ModField *F = new ModField(<long>modulus)
+-    cdef DenseMatrix *A = new DenseMatrix(F[0], <ModField.Element*>entries,<Py_ssize_t>nrows, <Py_ssize_t>ncols)
++    cdef DenseMatrix *A = new DenseMatrix(F[0], <Py_ssize_t>nrows, <Py_ssize_t>ncols, <ModField.Element*>entries)
+     cdef Py_ssize_t r = reducedRowEchelonize(A[0])
+     cdef Py_ssize_t i,j
+     for i in range(nrows):

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

@@ -0,0 +1,61 @@
+diff --git a/src/sage_docbuild/__init__.py b/src/sage_docbuild/__init__.py
+index b12d56a3c9..df9d949ed1 100644
+--- a/src/sage_docbuild/__init__.py
++++ b/src/sage_docbuild/__init__.py
+@@ -88,30 +88,6 @@ def builder_helper(type):
+     """
+     Return a function which builds the documentation for
+     output type ``type``.
+-
+-    TESTS:
+-
+-    Check that :trac:`25161` has been resolved::
+-
+-        sage: from sage_docbuild import DocBuilder, setup_parser
+-        sage: DocBuilder._options = setup_parser().parse_args([]) # builder_helper needs _options to be set
+-
+-        sage: import sage_docbuild.sphinxbuild
+-        sage: def raiseBaseException():
+-        ....:     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:  # 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)
+-        True
+     """
+     def f(self, *args, **kwds):
+         output_dir = self._output_dir(type)
+@@ -139,10 +115,9 @@ def builder_helper(type):
+         logger.debug(build_command)
+ 
+         # Run Sphinx with Sage's special logger
+-        sys.argv = ["sphinx-build"] + build_command.split()
+-        from .sphinxbuild import runsphinx
++        args = "python3 -um sage_docbuild.sphinxbuild -N".split() + build_command.split()
+         try:
+-            runsphinx()
++            subprocess.check_call(args)
+         except Exception:
+             if ABORT_ON_ERROR:
+                 raise
+diff --git a/src/sage_docbuild/sphinxbuild.py b/src/sage_docbuild/sphinxbuild.py
+index a39c99ffe9..73be823684 100644
+--- a/src/sage_docbuild/sphinxbuild.py
++++ b/src/sage_docbuild/sphinxbuild.py
+@@ -330,3 +330,8 @@ def runsphinx():
+         sys.stderr = saved_stderr
+         sys.stdout.flush()
+         sys.stderr.flush()
++
++if __name__ == '__main__':
++    import sys
++    sys.argv[0] = "sphinx-build"
++    runsphinx()

pkgs/applications/science/math/sage/patches/sympow-cache.patch

@@ -0,0 +1,21 @@
+diff --git a/src/sage/lfunctions/sympow.py b/src/sage/lfunctions/sympow.py
+index 92cb01fd73..b123e6accc 100644
+--- a/src/sage/lfunctions/sympow.py
++++ b/src/sage/lfunctions/sympow.py
+@@ -50,6 +50,7 @@ from __future__ import print_function, absolute_import
+ 
+ import os
+ 
++from sage.env import DOT_SAGE
+ from sage.structure.sage_object import SageObject
+ from sage.misc.all import pager
+ from sage.misc.verbose import verbose
+@@ -78,7 +79,7 @@ class Sympow(SageObject):
+         """
+         Used to call sympow with given args
+         """
+-        cmd = 'sympow %s' % args
++        cmd = 'env SYMPOW_CACHEDIR="%s/sympow///" sympow %s' % (DOT_SAGE, args)
+         with os.popen(cmd) as f:
+             v = f.read().strip()
+         verbose(v, level=2)

pkgs/applications/science/math/sage/patches/tachyon-renamed-focallength.patch

@@ -0,0 +1,81 @@
+diff --git a/src/sage/interfaces/tachyon.py b/src/sage/interfaces/tachyon.py
+index 3f1dcdb538..b6fa8d1fbd 100644
+--- a/src/sage/interfaces/tachyon.py
++++ b/src/sage/interfaces/tachyon.py
+@@ -261,13 +261,13 @@ written in the sequence they are listed in the examples in this section.
+   The {\bf PROJECTION} keyword must be followed by one of the supported
+ camera projection mode identifiers {\bf PERSPECTIVE}, {\bf PERSPECTIVE_DOF},
+ {\bf ORTHOGRAPHIC}, or {\bf FISHEYE}.  The {\bf FISHEYE} projection mode
+-requires two extra parameters {\bf FOCALLENGTH} and {\bf APERTURE}
++requires two extra parameters {\bf FOCALDIST} and {\bf APERTURE}
+ which precede the regular camera options.
+ 
+ \begin{verbatim}
+ Camera
+   projection perspective_dof
+-  focallength 0.75
++  focaldist 0.75
+   aperture 0.02
+   Zoom 0.666667
+   Aspectratio 1.000000
+diff --git a/src/sage/plot/plot3d/tachyon.py b/src/sage/plot/plot3d/tachyon.py
+index 08caf38d67..3e827411ce 100644
+--- a/src/sage/plot/plot3d/tachyon.py
++++ b/src/sage/plot/plot3d/tachyon.py
+@@ -92,7 +92,7 @@ angle, right angle)::
+ Finally there is the ``projection='perspective_dof'`` option. ::
+ 
+     sage: T = Tachyon(xres=800, antialiasing=4, raydepth=10,
+-    ....: projection='perspective_dof', focallength='1.0', aperture='.0025')
++    ....: projection='perspective_dof', focaldist='1.0', aperture='.0025')
+     sage: T.light((0,5,7), 1.0, (1,1,1))
+     sage: T.texture('t1', opacity=1, specular=.3)
+     sage: T.texture('t2', opacity=1, specular=.3, color=(0,0,1))
+@@ -186,7 +186,7 @@ class Tachyon(WithEqualityById, SageObject):
+       or ``'fisheye'``.
+     - ``frustum`` - (default ''), otherwise list of four numbers. Only
+       used with projection='fisheye'.
+-    - ``focallength`` - (default ''), otherwise a number. Only used
++    - ``focaldist`` - (default ''), otherwise a number. Only used
+       with projection='perspective_dof'.
+     - ``aperture`` - (default ''), otherwise a number.  Only used
+       with projection='perspective_dof'.
+@@ -331,7 +331,7 @@ class Tachyon(WithEqualityById, SageObject):
+     Use of the ``projection='perspective_dof'`` option.  This may not be
+     implemented correctly. ::
+ 
+-        sage: T = Tachyon(xres=800,antialiasing=4, raydepth=10, projection='perspective_dof', focallength='1.0', aperture='.0025')
++        sage: T = Tachyon(xres=800,antialiasing=4, raydepth=10, projection='perspective_dof', focaldist='1.0', aperture='.0025')
+         sage: T.light((0,5,7), 1.0, (1,1,1))
+         sage: T.texture('t1', opacity=1, specular=.3)
+         sage: T.texture('t2', opacity=1, specular=.3, color=(0,0,1))
+@@ -365,7 +365,7 @@ class Tachyon(WithEqualityById, SageObject):
+                  look_at=[0, 0, 0],
+                  viewdir=None,
+                  projection='PERSPECTIVE',
+-                 focallength='',
++                 focaldist='',
+                  aperture='',
+                  frustum=''):
+         r"""
+@@ -391,7 +391,7 @@ class Tachyon(WithEqualityById, SageObject):
+             self._camera_position = (-3, 0, 0) # default value
+         self._updir = updir
+         self._projection = projection
+-        self._focallength = focallength
++        self._focaldist = focaldist
+         self._aperture = aperture
+         self._frustum = frustum
+         self._objects = []
+@@ -624,9 +624,9 @@ class Tachyon(WithEqualityById, SageObject):
+         camera_out = r"""
+            camera
+               projection %s""" % (tostr(self._projection))
+-        if self._focallength != '':
++        if self._focaldist != '':
+             camera_out = camera_out + r"""
+-              focallength %s""" % (float(self._focallength))
++              focaldist %s""" % (float(self._focaldist))
+         if self._aperture != '':
+             camera_out = camera_out + r"""
+               aperture %s""" % (float(self._aperture))

pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix

@@ -0,0 +1,30 @@
+{ lib
+, buildPythonPackage
+, sage-src
+, sphinx
+, jupyter-sphinx
+}:
+
+buildPythonPackage rec {
+  version = src.version;
+  pname = "sage-docbuild";
+  src = sage-src;
+
+  propagatedBuildInputs = [
+    sphinx
+    jupyter-sphinx
+  ];
+
+  preBuild = ''
+    cd pkgs/sage-docbuild
+  '';
+
+  doCheck = false; # we will run tests in sagedoc.nix
+
+  meta = with lib; {
+    description = "Build system of the Sage documentation";
+    homepage = "https://www.sagemath.org";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+  };
+}

pkgs/applications/science/math/sage/python-modules/sage-setup.nix

@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, sage-src
+, pkgconfig # the python module, not the pkg-config alias
+}:
+
+buildPythonPackage rec {
+  version = src.version;
+  pname = "sage-setup";
+  src = sage-src;
+
+  buildInputs = [
+    pkgconfig
+  ];
+
+  preBuild = ''
+    cd pkgs/sage-setup
+  '';
+
+  doCheck = false; # sagelib depends on sage-setup, but sage-setup's tests depend on sagelib
+
+  meta = with lib; {
+    description = "Build system of the Sage library";
+    homepage = "https://www.sagemath.org";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+  };
+}

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

@@ -0,0 +1,194 @@
+{ stdenv
+, lib
+, writeTextFile
+, sagelib
+, sage-docbuild
+, env-locations
+, gfortran
+, bash
+, coreutils
+, gnused
+, gnugrep
+, binutils
+, pythonEnv
+, python3
+, pkg-config
+, pari
+, gap
+, maxima
+, singular
+, fflas-ffpack
+, givaro
+, gd
+, libpng
+, linbox
+, m4ri
+, giac
+, palp
+, rWrapper
+, gfan
+, cddlib
+, jmol
+, tachyon
+, glpk
+, eclib
+, sympow
+, nauty
+, sqlite
+, ppl
+, ecm
+, lcalc
+, rubiks
+, flintqs
+, blas
+, lapack
+, flint
+, gmp
+, mpfr
+, zlib
+, gsl
+, ntl
+, jdk
+, less
+}:
+
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+# This generates a `sage-env` shell file that will be sourced by sage on startup.
+# It sets up various environment variables, telling sage where to find its
+# dependencies.
+
+let
+  runtimepath = (lib.makeBinPath ([
+    "@sage-local@"
+    "@sage-local@/build"
+    pythonEnv
+    gfortran # for inline fortran
+    stdenv.cc # for cython
+    bash
+    coreutils
+    gnused
+    gnugrep
+    binutils.bintools
+    pkg-config
+    pari
+    gap
+    maxima.lisp-compiler
+    maxima
+    singular
+    giac
+    palp
+    # needs to be rWrapper since the default `R` doesn't include R's default libraries
+    rWrapper
+    gfan
+    cddlib
+    jmol
+    tachyon
+    glpk
+    eclib
+    sympow
+    nauty
+    sqlite
+    ppl
+    ecm
+    lcalc
+    rubiks
+    flintqs
+    jdk # only needed for `jmol` which may be replaced in the future
+    less # needed to prevent transient test errors until https://github.com/ipython/ipython/pull/11864 is resolved
+  ]
+  ));
+in
+writeTextFile rec {
+  name = "sage-env";
+  destination = "/${name}";
+  text = ''
+    export PKG_CONFIG_PATH='${lib.makeSearchPathOutput "dev" "lib/pkgconfig" [
+        # This should only be needed during build. However, since the  doctests
+        # also test the cython build (for example in src/sage/misc/cython.py),
+        # it is also needed for the testsuite to pass. We could fix the
+        # testsuite instead, but since all the packages are also runtime
+        # dependencies it doesn't really hurt to include them here.
+        singular
+        blas lapack
+        fflas-ffpack givaro
+        gd
+        libpng zlib
+        gsl
+        linbox
+        m4ri
+      ]
+    }'
+    export SAGE_ROOT='${sagelib.src}'
+  '' +
+    # TODO: is using pythonEnv instead of @sage-local@ here a good
+    # idea? there is a test in src/sage/env.py that checks if the values
+    # SAGE_ROOT and SAGE_LOCAL set here match the ones set in env.py.
+    # we fix up env.py's SAGE_ROOT in sage-src.nix (which does not
+    # have access to sage-with-env), but env.py autodetects
+    # SAGE_LOCAL to be pythonEnv.
+    # setting SAGE_LOCAL to pythonEnv also avoids having to create
+    # python3, ipython, ipython3 and jupyter symlinks in
+    # sage-with-env.nix.
+  ''
+    export SAGE_LOCAL='${pythonEnv}'
+
+    export SAGE_SHARE='${sagelib}/share'
+    export SAGE_ENV_CONFIG_SOURCED=1 # sage-env complains if sage-env-config is not sourced beforehand
+    orig_path="$PATH"
+    export PATH='${runtimepath}'
+
+    # set dependent vars, like JUPYTER_CONFIG_DIR
+    source "${sagelib.src}/src/bin/sage-env"
+    export PATH="$RUNTIMEPATH_PREFIX:${runtimepath}:$orig_path" # sage-env messes with PATH
+
+    export SAGE_LOGS="$TMPDIR/sage-logs"
+    export SAGE_DOC="''${SAGE_DOC_OVERRIDE:-doc-placeholder}"
+    export SAGE_DOC_SRC="''${SAGE_DOC_SRC_OVERRIDE:-${sagelib.src}/src/doc}"
+
+    # set locations of dependencies
+    . ${env-locations}/sage-env-locations
+
+    # needed for cython
+    export CC='${stdenv.cc}/bin/${stdenv.cc.targetPrefix}cc'
+    export CXX='${stdenv.cc}/bin/${stdenv.cc.targetPrefix}c++'
+    # cython needs to find these libraries, otherwise will fail with `ld: cannot find -lflint` or similar
+    export LDFLAGS='${
+      lib.concatStringsSep " " (map (pkg: "-L${pkg}/lib") [
+        flint
+        gap
+        glpk
+        gmp
+        mpfr
+        pari
+        zlib
+        eclib
+        gsl
+        ntl
+        jmol
+        sympow
+      ])
+    }'
+    export CFLAGS='${
+      lib.concatStringsSep " " (map (pkg: "-isystem ${pkg}/include") [
+        singular
+        gmp.dev
+        glpk
+        flint
+        gap
+        mpfr.dev
+      ])
+    }'
+    export CXXFLAGS=$CFLAGS
+
+    export SAGE_LIB='${sagelib}/${python3.sitePackages}'
+
+    export SAGE_EXTCODE='${sagelib.src}/src/sage/ext_data'
+
+  # for find_library
+    export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular giac]}''${DYLD_LIBRARY_PATH:+:}$DYLD_LIBRARY_PATH"
+  '';
+} // { # equivalent of `passthru`, which `writeTextFile` doesn't support
+  lib = sagelib;
+  docbuild = sage-docbuild;
+}

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

@@ -0,0 +1,150 @@
+{ stdenv
+, fetchFromGitHub
+, fetchpatch
+, runtimeShell
+}:
+
+# This file is responsible for fetching the sage source and adding necessary patches.
+# It does not actually build anything, it just copies the patched sources to $out.
+# This is done because multiple derivations rely on these sources and they should
+# all get the same sources with the same patches applied.
+
+let
+  # Fetch a diff between `base` and `rev` on sage's git server.
+  # Used to fetch trac tickets by setting the `base` to the last release and the
+  # `rev` to the last commit of the ticket.
+  #
+  # We don't use sage's own build system (which builds all its
+  # dependencies), so we exclude changes to "build/" from patches by
+  # default to avoid conflicts.
+  fetchSageDiff = { base, name, rev, sha256, squashed ? false, excludes ? [ "build/*" ]
+                  , ...}@args: (
+    fetchpatch ({
+      inherit name sha256 excludes;
+
+      # There are three places to get changes from:
+      #
+      # 1) From Sage's Trac. Contains all release tags (like "9.4") and all developer
+      # branches (wip patches from tickets), but exports each commit as a separate
+      # patch, so merge commits can lead to conflicts. Used if squashed == false.
+      #
+      # The above is the preferred option. To use it, find a Trac ticket and pass the
+      # "Commit" field from the ticket as "rev", choosing "base" as an appropriate
+      # release tag, i.e. a tag that doesn't cause the patch to include a lot of
+      # unrelated changes. If there is no such tag (due to nonlinear history, for
+      # example), there are two other options, listed below.
+      #
+      # 2) From GitHub's sagemath/sage repo. This lets us use a GH feature that allows
+      # us to choose between a .patch file, with one patch per commit, or a .diff file,
+      # which squashes all commits into a single diff. This is used if squashed ==
+      # true. This repo has all release tags. However, it has no developer branches, so
+      # this option can't be used if a change wasn't yet shipped in a (possibly beta)
+      # release.
+      #
+      # 3) From GitHub's sagemath/sagetrac-mirror repo. Mirrors all developer branches,
+      # but has no release tags. The only use case not covered by 1 or 2 is when we need
+      # to apply a patch from an open ticket that contains merge commits.
+      #
+      # Item 3 could cover all use cases if the sagemath/sagetrack-mirror repo had
+      # release tags, but it requires a sha instead of a release number in "base", which
+      # is inconvenient.
+      urls = if squashed
+             then [
+               "https://github.com/sagemath/sage/compare/${base}...${rev}.diff"
+               "https://github.com/sagemath/sagetrac-mirror/compare/${base}...${rev}.diff"
+             ]
+             else [ "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}" ];
+    } // builtins.removeAttrs args [ "rev" "base" "sha256" "squashed" "excludes" ])
+  );
+in
+stdenv.mkDerivation rec {
+  version = "9.6";
+  pname = "sage-src";
+
+  src = fetchFromGitHub {
+    owner = "sagemath";
+    repo = "sage";
+    rev = version;
+    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 = [
+    # Fixes a potential race condition which can lead to transient doctest failures.
+    ./patches/fix-ecl-race.patch
+
+    # Not necessary since library location is set explicitly
+    # https://trac.sagemath.org/ticket/27660#ticket
+    ./patches/do-not-test-find-library.patch
+
+    # Parallelize docubuild using subprocesses, fixing an isolation issue. See
+    # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
+    ./patches/sphinx-docbuild-subprocesses.patch
+  ];
+
+  # Since sage unfortunately does not release bugfix releases, packagers must
+  # fix those bugs themselves. This is for critical bugfixes, where "critical"
+  # == "causes (transient) doctest failures / somebody complained".
+  bugfixPatches = [
+    # To help debug the transient error in
+    # https://trac.sagemath.org/ticket/23087 when it next occurs.
+    ./patches/configurationpy-error-verbose.patch
+  ];
+
+  # Patches needed because of package updates. We could just pin the versions of
+  # dependencies, but that would lead to rebuilds, confusion and the burdons of
+  # maintaining multiple versions of dependencies. Instead we try to make sage
+  # compatible with never dependency versions when possible. All these changes
+  # should come from or be proposed to upstream. This list will probably never
+  # be empty since dependencies update all the time.
+  packageUpgradePatches = [
+    # After updating smypow to (https://trac.sagemath.org/ticket/3360) we can
+    # now set the cache dir to be within the .sage directory. This is not
+    # strictly necessary, but keeps us from littering in the user's HOME.
+    ./patches/sympow-cache.patch
+
+    # Upstream will wait until Sage 9.7 to upgrade to linbox 1.7 because it
+    # does not support gcc 6. We can upgrade earlier.
+    # https://trac.sagemath.org/ticket/32959
+    ./patches/linbox-1.7-upgrade.patch
+
+    # adapted from https://trac.sagemath.org/ticket/23712#comment:22
+    ./patches/tachyon-renamed-focallength.patch
+
+    # docutils 0.18.1 now triggers Sphinx warnings. tolerate them for
+    # 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
+  ];
+
+  patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;
+
+  postPatch = ''
+    # 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_ROOT\".*|var(\"SAGE_ROOT\", \"$out\")|" \
+      src/sage/env.py
+
+    # src/doc/en/reference/spkg/conf.py expects index.rst in its directory,
+    # a list of external packages in the sage distribution (build/pkgs)
+    # generated by the bootstrap script (which we don't run).  this is not
+    # relevant for other distributions, so remove it.
+    rm src/doc/en/reference/spkg/conf.py
+    sed -i "/spkg/d" src/doc/en/reference/index.rst
+
+    # the bootstrap script also generates installation instructions for
+    # arch, debian, fedora, cygwin and homebrew using data from build/pkgs.
+    # we don't run the bootstrap script, so disable including the generated
+    # files. docbuilding fails otherwise.
+    sed -i "/literalinclude/d" src/doc/en/installation/source.rst
+  '';
+
+  buildPhase = "# do nothing";
+
+  installPhase = ''
+    cp -r . "$out"
+  '';
+}

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

@@ -0,0 +1,61 @@
+{ stdenv
+, lib
+, sage-with-env
+, makeWrapper
+, files ? null # "null" means run all tests
+, longTests ? true # run tests marked as "long time" (roughly doubles runtime)
+# Run as many tests as possible in approximately n seconds. This will give each
+# file to test a "time budget" and stop tests if it is exceeded. 300 is the
+# upstream default value.
+# https://trac.sagemath.org/ticket/25270 for details.
+, timeLimit ? null
+}:
+
+# for a quick test of some source files:
+# nix-build -E 'with (import ./. {}); sage.tests.override { files = [ "src/sage/misc/cython.py" ];}'
+
+let
+  src = sage-with-env.env.lib.src;
+  runAllTests = files == null;
+  testArgs = if runAllTests then "--all" else testFileList;
+  patienceSpecifier = if longTests then "--long" else "";
+  timeSpecifier = if timeLimit == null then "" else "--short ${toString timeLimit}";
+  relpathToArg = relpath: lib.escapeShellArg "${src}/${relpath}"; # paths need to be absolute
+  testFileList = lib.concatStringsSep " " (map relpathToArg files);
+in
+stdenv.mkDerivation {
+  version = src.version;
+  pname = "sage-tests";
+  inherit src;
+
+  buildInputs = [
+    makeWrapper
+    sage-with-env
+  ];
+
+  dontUnpack = true;
+  configurePhase = "#do nothing";
+  buildPhase = "#do nothing";
+
+  installPhase = ''
+    # This output is not actually needed for anything, the package just
+    # exists to decouple the sage build from its t ests.
+
+    mkdir -p "$out/bin"
+    # Like a symlink, but make sure that $0 points to the original.
+    makeWrapper "${sage-with-env}/bin/sage" "$out/bin/sage"
+  '';
+
+  doInstallCheck = true;
+  installCheckPhase = ''
+    export HOME="$TMPDIR/sage-home"
+    mkdir -p "$HOME"
+
+    # avoid running out of memory with many threads in subprocesses, see
+    # https://github.com/NixOS/nixpkgs/pull/65802
+    export GLIBC_TUNABLES=glibc.malloc.arena_max=4
+
+    echo "Running sage tests with arguments ${timeSpecifier} ${patienceSpecifier} ${testArgs}"
+    "sage" -t --timeout=0 --nthreads "$NIX_BUILD_CORES" --optional=sage ${timeSpecifier} ${patienceSpecifier} ${testArgs}
+  '';
+}

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

@@ -0,0 +1,139 @@
+{ stdenv
+, lib
+, makeWrapper
+, sage-env
+, blas
+, lapack
+, pkg-config
+, three
+, singular
+, gap
+, giac
+, maxima
+, pari
+, gmp
+, gfan
+, python3
+, flintqs
+, eclib
+, ntl
+, ecm
+, pythonEnv
+}:
+
+# lots of segfaults with (64 bit) blas
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+# Wrapper that combined `sagelib` with `sage-env` to produce an actually
+# executable sage. No tests are run yet and no documentation is built.
+
+let
+  buildInputs = [
+    pythonEnv # for patchShebangs
+    makeWrapper
+    pkg-config
+    blas lapack
+    singular
+    three
+    giac
+    gap
+    pari
+    gmp
+    gfan
+    maxima
+    eclib
+    flintqs
+    ntl
+    ecm
+  ];
+
+  # remove python prefix, replace "-" in the name by "_", apply patch_names
+  # python3.8-some-pkg-1.0 -> some_pkg-1.0
+  pkg_to_spkg_name = pkg: patch_names: let
+    parts = lib.splitString "-" pkg.name;
+    # remove python3.8-
+    stripped_parts = if (builtins.head parts) == python3.libPrefix then builtins.tail parts else parts;
+    version = lib.last stripped_parts;
+    orig_pkgname = lib.init stripped_parts;
+    pkgname = patch_names (lib.concatStringsSep "_" orig_pkgname);
+  in pkgname + "-" + version;
+
+
+  # return the names of all dependencies in the transitive closure
+  transitiveClosure = dep:
+  if dep == null then
+    # propagatedBuildInputs might contain null
+    # (although that might be considered a programming error in the derivation)
+    []
+  else
+    [ dep ] ++ (
+      if builtins.hasAttr "propagatedBuildInputs" dep then
+        lib.unique (builtins.concatLists (map transitiveClosure dep.propagatedBuildInputs))
+      else
+      []
+    );
+
+  allInputs = lib.remove null (buildInputs ++ pythonEnv.extraLibs);
+  transitiveDeps = lib.unique (builtins.concatLists (map transitiveClosure allInputs ));
+  # fix differences between spkg and sage names
+  # (could patch sage instead, but this is more lightweight and also works for packages depending on sage)
+  patch_names = builtins.replaceStrings [
+    "zope.interface"
+    "node_three"
+  ] [
+    "zope_interface"
+    "threejs"
+  ];
+  # spkg names (this_is_a_package-version) of all transitive deps
+  input_names = map (dep: pkg_to_spkg_name dep patch_names) transitiveDeps;
+in
+stdenv.mkDerivation rec {
+  version = src.version;
+  pname = "sage-with-env";
+  src = sage-env.lib.src;
+
+  inherit buildInputs;
+
+  configurePhase = "#do nothing";
+
+  buildPhase = ''
+    mkdir installed
+    for pkg in ${lib.concatStringsSep " " input_names}; do
+      touch "installed/$pkg"
+    done
+
+    # threejs version is in format 0.<version>.minor, but sage currently still
+    # relies on installed_packages for the online version of threejs to work
+    # and expects the format r<version>. This is a hotfix for now.
+    # upstream: https://trac.sagemath.org/ticket/26434
+    rm "installed/threejs"*
+    touch "installed/threejs-r${lib.versions.minor three.version}"
+  '';
+
+  installPhase = ''
+    mkdir -p "$out/var/lib/sage"
+    cp -r installed "$out/var/lib/sage"
+
+    mkdir -p "$out/etc"
+    # sage tests will try to create this file if it doesn't exist
+    touch "$out/etc/sage-started.txt"
+
+    mkdir -p "$out/build"
+
+    # the scripts in src/bin will find the actual sage source files using environment variables set in `sage-env`
+    cp -r src/bin "$out/bin"
+    cp -r build/bin "$out/build/bin"
+
+    # sage assumes the existence of sage-src-env-config.in means it's being executed in-tree. in this case, it
+    # adds SAGE_SRC/bin to PATH, breaking our wrappers
+    rm "$out/bin"/*.in "$out/build/bin"/*.in
+
+    cp -f '${sage-env}/sage-env' "$out/bin/sage-env"
+    substituteInPlace "$out/bin/sage-env" \
+      --subst-var-by sage-local "$out"
+  '';
+
+  passthru = {
+    env = sage-env;
+  };
+}

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

@@ -0,0 +1,62 @@
+{ lib, stdenv
+, makeWrapper
+, sage-tests
+, sage-with-env
+, jupyter-kernel-definition
+, jupyter-kernel-specs
+, sagedoc
+, withDoc
+, requireSageTests
+}:
+
+# A wrapper that makes sure sage finds its docs (if they were build) and the
+# jupyter kernel spec.
+
+stdenv.mkDerivation rec {
+  version = src.version;
+  pname = "sage";
+  src = sage-with-env.env.lib.src;
+
+  buildInputs = [
+    makeWrapper
+  ] ++ lib.optionals requireSageTests [
+    # This is a hack to make sure sage-tests is evaluated. It doesn't acutally
+    # produce anything of value, it just decouples the tests from the build.
+    sage-tests
+  ];
+
+  dontUnpack = true;
+  configurePhase = "#do nothing";
+  buildPhase = "#do nothing";
+
+  installPhase = ''
+    mkdir -p "$out/bin"
+    makeWrapper "${sage-with-env}/bin/sage" "$out/bin/sage" \
+      --set SAGE_DOC_SRC_OVERRIDE "${src}/src/doc" ${
+        lib.optionalString withDoc "--set SAGE_DOC_OVERRIDE ${sagedoc}/share/doc/sage"
+      } \
+      --prefix JUPYTER_PATH : "${jupyter-kernel-specs}"
+  '';
+
+  doInstallCheck = withDoc;
+  installCheckPhase = ''
+    export HOME="$TMPDIR/sage-home"
+    mkdir -p "$HOME"
+    "$out/bin/sage" -c 'browse_sage_doc._open("reference", testing=True)'
+  '';
+
+  passthru = {
+    tests = sage-tests;
+    quicktest = sage-tests.override { longTests = false; timeLimit = 600; }; # as many tests as possible in ~10m
+    doc = sagedoc;
+    lib = sage-with-env.env.lib;
+    kernelspec = jupyter-kernel-definition;
+  };
+
+  meta = with lib; {
+    description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab";
+    homepage = "https://www.sagemath.org";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+  };
+}

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

@@ -0,0 +1,71 @@
+{ stdenv
+, sage-with-env
+, python3
+, jupyter-kernel-specs
+}:
+
+stdenv.mkDerivation rec {
+  version = src.version;
+  pname = "sagedoc";
+  src = sage-with-env.env.lib.src;
+
+  strictDeps = true;
+
+  unpackPhase = ''
+    export SAGE_DOC_OVERRIDE="$PWD/share/doc/sage"
+    export SAGE_DOC_SRC_OVERRIDE="$PWD/docsrc"
+
+    cp -r "${src}/src/doc" "$SAGE_DOC_SRC_OVERRIDE"
+    chmod -R 755 "$SAGE_DOC_SRC_OVERRIDE"
+  '';
+
+  buildPhase = ''
+    export SAGE_NUM_THREADS="$NIX_BUILD_CORES"
+    export HOME="$TMPDIR/sage_home"
+    mkdir -p "$HOME"
+
+    # needed to link them in the sage docs using intersphinx
+    export PPLPY_DOCS=${python3.pkgs.pplpy.doc}/share/doc/pplpy
+
+    # adapted from src/doc/bootstrap (which we don't run)
+    OUTPUT_DIR="$SAGE_DOC_SRC_OVERRIDE/en/reference/repl"
+    mkdir -p "$OUTPUT_DIR"
+    OUTPUT="$OUTPUT_DIR/options.txt"
+    ${sage-with-env}/bin/sage -advanced > "$OUTPUT"
+
+    # jupyter-sphinx calls the sagemath jupyter kernel during docbuild
+    export JUPYTER_PATH=${jupyter-kernel-specs}
+
+    # sage --docbuild unsets JUPYTER_PATH, so we call sage_docbuild directly
+    # https://trac.sagemath.org/ticket/33650#comment:32
+    ${sage-with-env}/bin/sage --python3 -m sage_docbuild \
+      --mathjax \
+      --no-pdf-links \
+      all html < /dev/null
+  '';
+
+  installPhase = ''
+    cd "$SAGE_DOC_OVERRIDE"
+
+    mkdir -p "$out/share/doc/sage"
+    cp -r html "$out"/share/doc/sage
+
+    # Replace duplicated files by symlinks (Gentoo)
+    cd "$out"/share/doc/sage
+    mv html/en/_static{,.tmp}
+    for _dir in `find -name _static` ; do
+          rm -r $_dir
+          ln -rs html/en/_static $_dir
+    done
+    mv html/en/_static{.tmp,}
+  '';
+
+  doCheck = true;
+  checkPhase = ''
+    # 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
+  '';
+}

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

@@ -0,0 +1,213 @@
+{ sage-src
+, env-locations
+, perl
+, buildPythonPackage
+, m4
+, arb
+, blas
+, lapack
+, brial
+, cliquer
+, cypari2
+, cysignals
+, cython
+, lisp-compiler
+, eclib
+, ecm
+, flint
+, gd
+, giac
+, givaro
+, glpk
+, gsl
+, iml
+, jinja2
+, lcalc
+, lrcalc
+, gap
+, linbox
+, m4ri
+, m4rie
+, memory-allocator
+, libmpc
+, mpfi
+, ntl
+, numpy
+, pari
+, pkgconfig # the python module, not the pkg-config alias
+, pkg-config
+, planarity
+, ppl
+, primecountpy
+, python
+, ratpoints
+, readline
+, rankwidth
+, symmetrica
+, zn_poly
+, fflas-ffpack
+, boost
+, singular
+, pip
+, jupyter_core
+, sage-setup
+, libhomfly
+, libbraiding
+, gmpy2
+, pplpy
+, sqlite
+, jupyter-client
+, ipywidgets
+, mpmath
+, rpy2
+, fpylll
+, scipy
+, sympy
+, matplotlib
+, pillow
+, ipykernel
+, networkx
+, ptyprocess
+, lrcalc-python
+, sphinx # TODO: this is in setup.cfg, should we override it?
+}:
+
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+# This is the core sage python package. Everything else is just wrappers gluing
+# stuff together. It is not very useful on its own though, since it will not
+# find many of its dependencies without `sage-env`, will not be tested without
+# `sage-tests` and will not have html docs without `sagedoc`.
+
+buildPythonPackage rec {
+  version = src.version;
+  pname = "sagelib";
+  src = sage-src;
+
+  nativeBuildInputs = [
+    iml
+    perl
+    jupyter_core
+    pkg-config
+    sage-setup
+    pip # needed to query installed packages
+    lisp-compiler
+    m4
+  ];
+
+  buildInputs = [
+    gd
+    readline
+    iml
+  ];
+
+  propagatedBuildInputs = [
+    cypari2
+    jinja2
+    numpy
+    pkgconfig
+    boost
+    arb
+    brial
+    cliquer
+    lisp-compiler
+    eclib
+    ecm
+    fflas-ffpack
+    flint
+    giac
+    givaro
+    glpk
+    gsl
+    lcalc
+    gap
+    libmpc
+    linbox
+    lrcalc
+    m4ri
+    m4rie
+    memory-allocator
+    mpfi
+    ntl
+    blas
+    lapack
+    pari
+    planarity
+    ppl
+    primecountpy
+    rankwidth
+    ratpoints
+    singular
+    symmetrica
+    zn_poly
+    pip
+    cython
+    cysignals
+    libhomfly
+    libbraiding
+    gmpy2
+    pplpy
+    sqlite
+    mpmath
+    rpy2
+    scipy
+    sympy
+    matplotlib
+    pillow
+    ipykernel
+    fpylll
+    networkx
+    jupyter-client
+    ipywidgets
+    ptyprocess
+    lrcalc-python
+    sphinx
+  ];
+
+  preBuild = ''
+    export SAGE_ROOT="$PWD"
+    export SAGE_LOCAL="$SAGE_ROOT"
+    export SAGE_SHARE="$SAGE_LOCAL/share"
+
+    # set locations of dependencies (needed for nbextensions like threejs)
+    . ${env-locations}/sage-env-locations
+
+    export JUPYTER_PATH="$SAGE_LOCAL/jupyter"
+    export PATH="$SAGE_ROOT/build/bin:$SAGE_ROOT/src/bin:$PATH"
+
+    export SAGE_NUM_THREADS="$NIX_BUILD_CORES"
+
+    mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython"
+    mkdir -p "var/lib/sage/installed"
+
+    cd build/pkgs/sagelib
+
+    # some files, like Pipfile, pyproject.toml, requirements.txt and setup.cfg
+    # are generated by the bootstrap script using m4. these can fetch data from
+    # build/pkgs, either directly or via sage-get-system-packages.
+    sed -i '/sage_conf/d' src/setup.cfg.m4
+    sed -i '/sage_conf/d' src/requirements.txt.m4
+
+    # version lower bounds are useful, but upper bounds are a hassle because
+    # Sage tests already catch any relevant API breakage.
+    # according to the discussion at https://trac.sagemath.org/ticket/33520,
+    # upper bounds will be less noisy starting from Sage 9.6.
+    sed -i 's/==0.5.1/>=0.5.1/' ../ptyprocess/install-requires.txt
+    sed -i 's/, <[^, ]*//' ../*/install-requires.txt
+
+    for infile in src/*.m4; do
+        if [ -f "$infile" ]; then
+            outfile="src/$(basename $infile .m4)"
+            m4 "$infile" > "$outfile"
+        fi
+    done
+
+    cd src
+  '';
+
+  postInstall = ''
+    rm -r "$out/${python.sitePackages}/sage/cython_debug"
+  '';
+
+  doCheck = false; # we will run tests in sage-tests.nix
+}

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

@@ -0,0 +1,19 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  pname = "threejs-sage";
+  version = "r122";
+
+  src = fetchFromGitHub {
+    owner = "sagemath";
+    repo = "threejs-sage";
+    rev = version;
+    sha256 = "sha256-xPAPt36Fon3hYQq6SOmGkIyUzAII2LMl10nqYG4UPI0=";
+  };
+
+  installPhase = ''
+    mkdir -p "$out/lib/node_modules/three/"
+    cp version "$out/lib/node_modules/three"
+    cp -r build "$out/lib/node_modules/three/$(cat version)"
+  '';
+}