diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/math/sage/default.nix')
| -rw-r--r-- | nixpkgs/pkgs/applications/science/math/sage/default.nix | 172 |
1 files changed, 172 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/math/sage/default.nix b/nixpkgs/pkgs/applications/science/math/sage/default.nix new file mode 100644 index 000000000000..caf51c3da251 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/default.nix @@ -0,0 +1,172 @@ +{ pkgs +, withDoc ? false +}: + +# 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; + + # https://trac.sagemath.org/ticket/15980 for tracking of python3 support + python = pkgs.python2.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 sage-src env-locations pynac singular; + linbox = pkgs.linbox.override { withSage = true; }; + pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig + }; + }; + }; + + 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 = "${sage-src}/doc/common/themes/sage/static/sageicon.png"; + logo64 = "${sage-src}/doc/common/themes/sage/static/sageicon.png"; + }; + + # 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 singular maxima-ecl; + cysignals = python.pkgs.cysignals; + three = nodePackages.three; + 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 = python.pkgs.sagelib; + inherit env-locations; + inherit python ecl singular palp flint pynac pythonEnv maxima-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; + }; + + # 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 sage-env; + inherit pynac singular maxima-ecl; + pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig + three = nodePackages.three; + }; + + # 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 python.pkgs; [ + sagelib + pybrial + sagenb + cvxopt + networkx + service-identity + psutil + sympy + fpylll + matplotlib + tkinter # optional, as a matplotlib backend (use with `%matplotlib tk`) + scipy + ipywidgets + rpy2 + sphinx + typing + pillow + ]; + + pythonEnv = python.buildEnv.override { + extraLibs = pythonRuntimeDeps; + ignoreCollisions = true; + } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible + + arb = pkgs.arb.override { inherit flint; }; + + singular = pkgs.singular.override { inherit flint; }; + + # https://trac.sagemath.org/ticket/26625 + maxima-ecl = pkgs.maxima-ecl; + + # *not* to confuse with the python package "pynac" + pynac = pkgs.pynac.override { inherit singular flint; }; + + # 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 + ]; + }; + + # 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 { + inherit sage-tests sage-with-env sagedoc jupyter-kernel-definition; + inherit withDoc; +} |