nixpkgs/pkgs/applications/science/math/sage/default.nix
Jonathan Ringer 9bb3fccb5b treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix
continuation of #109595

pkgconfig was aliased in 2018, however, it remained in
all-packages.nix due to its wide usage. This cleans
up the remaining references to pkgs.pkgsconfig and
moves the entry to aliases.nix.

python3Packages.pkgconfig remained unchanged because
it's the canonical name of the upstream package
on pypi.
2021-01-19 01:16:25 -08:00

164 lines
5.3 KiB
Nix

{ 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;
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 pynac singular;
ecl = maxima-ecl.ecl;
linbox = pkgs.linbox.override { withSage = true; };
pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
};
};
};
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;
inherit singular maxima-ecl;
ecl = maxima-ecl.ecl;
cysignals = python3.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 = python3.pkgs.sagelib;
inherit env-locations;
inherit python3 singular palp flint pynac pythonEnv maxima-ecl;
ecl = maxima-ecl.ecl;
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;
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 python3 pythonEnv;
inherit sage-env;
inherit pynac singular maxima-ecl;
pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
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 python3.pkgs; [
sagelib
cvxopt
networkx
service-identity
psutil
sympy
fpylll
matplotlib
tkinter # optional, as a matplotlib backend (use with `%matplotlib tk`)
scipy
ipywidgets
rpy2
sphinx
pillow
];
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-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; };
# 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;
inherit withDoc;
}