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author | Alyssa Ross <hi@alyssa.is> | 2021-01-15 10:30:44 +0000 |
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committer | Alyssa Ross <hi@alyssa.is> | 2021-01-15 10:30:44 +0000 |
commit | e0794be8a0d11e90461e5a9c85012a36b93ec976 (patch) | |
tree | efd9cbc55ea3322867bf601c4d536758a3dd5fcc /nixpkgs/pkgs/applications/science/math/sage/default.nix | |
parent | 3538874082ded7647b1ccec0343c7c1e882cfef3 (diff) | |
parent | 1a57d96edd156958b12782e8c8b6a374142a7248 (diff) | |
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Merge commit '1a57d96edd156958b12782e8c8b6a374142a7248'
Diffstat (limited to 'nixpkgs/pkgs/applications/science/math/sage/default.nix')
-rw-r--r-- | nixpkgs/pkgs/applications/science/math/sage/default.nix | 65 |
1 files changed, 28 insertions, 37 deletions
diff --git a/nixpkgs/pkgs/applications/science/math/sage/default.nix b/nixpkgs/pkgs/applications/science/math/sage/default.nix index caf51c3da251..416f2b957b7b 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/default.nix +++ b/nixpkgs/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 { |