Timo Kaufmann
GitHub
commit
0c23fa9aaf
18 changed files with 239 additions and 378 deletions
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@ -2,46 +2,7 @@
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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.
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Don't feel discouraged to fix, simplify or improve things though. Here's a quick overview over the functions of the individual files:
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- `sage-src.nix`
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Downloads the source code and applies patches. This makes sure that all the other files work with the same sage source. If you want to apply a patch to sage or update sage to a new version, this is the place to do it.
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- `env-locations.nix`
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Creates a bash file that sets a bunch of environment variables telling sage where to find various packages and files. The definitions of those environment variables can be found in the sage source in the `src/env.py` file. This bash file needs to be sourced before sage is started (done in `sage-env.nix` and `sagedoc.nix`).
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- `sage-env.nix`
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Sets all environment variables sage needs to run. This includes the package locations defined in `env-locations.nix` as well as the location of sage itself and its various subdirectories.
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- `sagelib.nix`
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Defines the main sage package (without setting the necessary environments or running any tests).
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- `sage-with-env.nix`
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Wraps sage in the necessary environment.
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- `sage.nix`
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Runs sages doctests.
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- `sage-wrapper.nix`
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Optionally tells sage where do find the docs.
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- `sagedoc.nix`
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Builds and tests the sage html documentation. Can be used for offline documentation viewing as well as the sage `browse_sage_doc` and `search_doc` functions.
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- `sagenb.nix`
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The (semi deprecated) sage notebook.
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- `default.nix`
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Introduces necessary overrides, defines new packages and ties everything together (returning the `sage` package).
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- `flask-oldsessions.nix`, `flask-openid.nix`, `python-openid.nix`
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These are python packages that were rejected from the main nixpkgs tree because they appear unmaintained. They are needed for the (semi-deprecated) sage notebook. Since that notebook is still needed to run the sage doctests, these packages are included but not exposed to the rest of nixpkgs.
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- `pybrial.nix`
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pybrial is a dependency of sage. However, pybrial itself also has sage as a dependency. Because of that circular dependency, pybrial is hidden from the rest of nixpkgs (just as the flask packages and python-openid.
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- `openblas-pc.nix`
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This creates a `.pc` file to be read by `pkg-config` that allows openblas to take on different roles, like `cblas` or `lapack`.
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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.
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## The sage build is broken
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@ -1,68 +1,85 @@
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{ nixpkgs
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{ pkgs
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, withDoc ? false
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}:
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# Here sage and its dependencies are put together. Some dependencies may be pinned
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# as a last resort. Patching sage for compatibility with newer dependency versions
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# is always preferred, see `sage-src.nix` for that.
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let
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inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages;
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inherit (pkgs) fetchurl symlinkJoin callPackage nodePackages;
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# https://trac.sagemath.org/ticket/15980 for tracking of python3 support
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python = nixpkgs.python2.override {
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python = pkgs.python2.override {
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packageOverrides = self: super: {
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# python packages that appear unmaintained and were not accepted into the nixpkgs
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# tree because of that. These packages are only dependencies of the more-or-less
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# deprecated sagenb. However sagenb is still a default dependency and the doctests
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# depend on it.
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# See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion.
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# The dependency on the sage notebook (and therefore these packages) will be
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# removed in the future:
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# https://trac.sagemath.org/ticket/25837
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flask-oldsessions = self.callPackage ./flask-oldsessions.nix {};
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flask-openid = self.callPackage ./flask-openid.nix {};
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python-openid = self.callPackage ./python-openid.nix {};
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pybrial = self.callPackage ./pybrial.nix {};
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sagelib = self.callPackage ./sagelib.nix {
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inherit flint ecl arb;
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inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
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linbox = nixpkgs.linbox.override { withSage = true; };
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};
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sagenb = self.callPackage ./sagenb.nix {
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mathjax = nodePackages.mathjax;
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};
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sagedoc = self.callPackage ./sagedoc.nix {
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inherit sage-src;
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};
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# Package with a cyclic dependency with sage
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pybrial = self.callPackage ./pybrial.nix {};
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env-locations = self.callPackage ./env-locations.nix {
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inherit pari_data ecl;
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inherit singular;
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three = nodePackages.three;
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mathjax = nodePackages.mathjax;
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};
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sage-env = self.callPackage ./sage-env.nix {
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inherit sage-src python rWrapper openblas-cblas-pc ecl singular palp flint pynac pythonEnv;
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pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
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};
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sage-with-env = self.callPackage ./sage-with-env.nix {
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inherit pythonEnv;
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inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
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pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
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three = nodePackages.three;
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};
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sage = self.callPackage ./sage.nix { };
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sage-wrapper = self.callPackage ./sage-wrapper.nix {
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inherit sage-src withDoc;
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# `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
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sagelib = self.callPackage ./sagelib.nix {
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inherit flint ecl arb;
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inherit sage-src pynac singular;
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linbox = pkgs.linbox.override { withSage = true; };
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};
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};
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};
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openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; };
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openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; };
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openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; };
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# A bash script setting various environment variables to tell sage where
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# the files its looking fore are located. Also see `sage-env`.
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env-locations = callPackage ./env-locations.nix {
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inherit pari_data ecl;
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inherit singular;
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cysignals = python.pkgs.cysignals;
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three = nodePackages.three;
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mathjax = nodePackages.mathjax;
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};
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# The shell file that gets sourced on every sage start. Will also source
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# the env-locations file.
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sage-env = callPackage ./sage-env.nix {
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sagelib = python.pkgs.sagelib;
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inherit env-locations;
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inherit python rWrapper ecl singular palp flint pynac pythonEnv;
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pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
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};
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# The documentation for sage, building it takes a lot of ram.
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sagedoc = callPackage ./sagedoc.nix {
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inherit sage-with-env;
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inherit python;
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};
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# sagelib with added wrappers and a dependency on sage-tests to make sure thet tests were run.
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sage-with-env = callPackage ./sage-with-env.nix {
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inherit pythonEnv;
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inherit sage-env;
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inherit pynac singular;
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pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
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three = nodePackages.three;
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};
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# Doesn't actually build anything, just runs sages testsuite. This is a
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# separate derivation to make it possible to re-run the tests without
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# rebuilding sagelib (which takes ~30 minutes).
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# Running the tests should take something in the order of 1h.
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sage-tests = callPackage ./sage-tests.nix {
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inherit sage-with-env;
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};
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sage-src = callPackage ./sage-src.nix {};
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@ -91,9 +108,9 @@ let
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} // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
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# needs to be rWrapper, standard "R" doesn't include default packages
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rWrapper = nixpkgs.rWrapper.override {
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rWrapper = pkgs.rWrapper.override {
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# https://trac.sagemath.org/ticket/25674
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R = nixpkgs.R.overrideAttrs (attrs: rec {
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R = pkgs.R.overrideAttrs (attrs: rec {
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name = "R-3.4.4";
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src = fetchurl {
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url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
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@ -102,44 +119,45 @@ let
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});
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};
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arb = nixpkgs.arb.override { inherit flint; };
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arb = pkgs.arb.override { inherit flint; };
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singular = nixpkgs.singular.override { inherit flint; };
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singular = pkgs.singular.override { inherit flint; };
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# *not* to confuse with the python package "pynac"
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pynac = nixpkgs.pynac.override { inherit singular flint; };
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pynac = pkgs.pynac.override { inherit singular flint; };
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# With openblas (64 bit), the tests fail the same way as when sage is build with
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# openblas instead of openblasCompat. Apparently other packages somehow use flints
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# blas when it is available. Alternative would be to override flint to use
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# openblasCompat.
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flint = nixpkgs.flint.override { withBlas = false; };
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flint = pkgs.flint.override { withBlas = false; };
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# Multiple palp dimensions need to be available and sage expects them all to be
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# in the same folder.
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palp = symlinkJoin {
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name = "palp-${nixpkgs.palp.version}";
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name = "palp-${pkgs.palp.version}";
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paths = [
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(nixpkgs.palp.override { dimensions = 4; doSymlink = false; })
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(nixpkgs.palp.override { dimensions = 5; doSymlink = false; })
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(nixpkgs.palp.override { dimensions = 6; doSymlink = true; })
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(nixpkgs.palp.override { dimensions = 11; doSymlink = false; })
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(pkgs.palp.override { dimensions = 4; doSymlink = false; })
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(pkgs.palp.override { dimensions = 5; doSymlink = false; })
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(pkgs.palp.override { dimensions = 6; doSymlink = true; })
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(pkgs.palp.override { dimensions = 11; doSymlink = false; })
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];
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};
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# Sage expects those in the same directory.
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pari_data = symlinkJoin {
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name = "pari_data";
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paths = with nixpkgs; [
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paths = with pkgs; [
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pari-galdata
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pari-seadata-small
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];
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};
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# https://trac.sagemath.org/ticket/22191
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ecl = nixpkgs.ecl_16_1_2;
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ecl = pkgs.ecl_16_1_2;
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in
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python.pkgs.sage-wrapper // {
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doc = python.pkgs.sagedoc;
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lib = python.pkgs.sagelib;
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}
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# A wrapper around sage that makes sure sage finds its docs (if they were build).
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callPackage ./sage.nix {
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inherit sage-tests sage-with-env sagedoc;
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inherit withDoc;
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}
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@ -16,6 +16,8 @@
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, cysignals
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}:
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# A bash script setting various environment variables to tell sage where
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# the files its looking fore are located. Also see `sage-env`.
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writeTextFile rec {
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name = "sage-env-locations";
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destination = "/${name}";
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@ -1,17 +0,0 @@
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{ openblasCompat
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, writeTextFile
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, name
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}:
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writeTextFile {
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name = "openblas-${name}-pc-${openblasCompat.version}";
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destination = "/lib/pkgconfig/${name}.pc";
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text = ''
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Name: ${name}
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Version: ${openblasCompat.version}
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Description: ${name} for SageMath, provided by the OpenBLAS package.
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Cflags: -I${openblasCompat}/include
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Libs: -L${openblasCompat}/lib -lopenblas
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'';
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}
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@ -1,16 +0,0 @@
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diff --git a/src/sage/interfaces/mwrank.py b/src/sage/interfaces/mwrank.py
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index 4417b59276..ae57ca2991 100644
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--- a/src/sage/interfaces/mwrank.py
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+++ b/src/sage/interfaces/mwrank.py
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@@ -54,8 +54,9 @@ def Mwrank(options="", server=None, server_tmpdir=None):
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sage: M = Mwrank('-v 0 -l')
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sage: print(M('0 0 1 -1 0'))
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Curve [0,0,1,-1,0] : Rank = 1
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- Generator 1 is [0:-1:1]; height 0.0511114082399688
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- Regulator = 0.0511114082399688
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+ Generator 1 is [0:-1:1]; height 0.051111408239969
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+ Regulator = 0.051111408239969
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+
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"""
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global instances
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try:
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@ -1,98 +0,0 @@
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diff --git a/src/sage/libs/eclib/interface.py b/src/sage/libs/eclib/interface.py
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index f77000c478..9d17d412ae 100644
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--- a/src/sage/libs/eclib/interface.py
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+++ b/src/sage/libs/eclib/interface.py
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@@ -1014,7 +1014,7 @@ class mwrank_MordellWeil(SageObject):
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WARNING: saturation at primes p > 2 will not be done;
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...
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Gained index 2
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- New regulator = 93.857300720636393209
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+ New regulator = 93.85730...
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(False, 2, '[ ]')
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sage: EQ.points()
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[[-2, 3, 1], [2707496766203306, 864581029138191, 2969715140223272], [-13422227300, -49322830557, 12167000000]]
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@@ -1025,7 +1025,7 @@ class mwrank_MordellWeil(SageObject):
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WARNING: saturation at primes p > 3 will not be done;
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...
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Gained index 3
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- New regulator = 10.4285889689595992455
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+ New regulator = 10.42858...
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(False, 3, '[ ]')
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sage: EQ.points()
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[[-2, 3, 1], [-14, 25, 8], [-13422227300, -49322830557, 12167000000]]
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@@ -1036,7 +1036,7 @@ class mwrank_MordellWeil(SageObject):
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WARNING: saturation at primes p > 5 will not be done;
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...
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Gained index 5
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- New regulator = 0.417143558758383969818
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+ New regulator = 0.41714...
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(False, 5, '[ ]')
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sage: EQ.points()
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[[-2, 3, 1], [-14, 25, 8], [1, -1, 1]]
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@@ -1221,7 +1221,7 @@ class mwrank_MordellWeil(SageObject):
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WARNING: saturation at primes p > 2 will not be done;
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...
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Gained index 2
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- New regulator = 93.857300720636393209
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+ New regulator = 93.85730...
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(False, 2, '[ ]')
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sage: EQ
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Subgroup of Mordell-Weil group: [[-2:3:1], [2707496766203306:864581029138191:2969715140223272], [-13422227300:-49322830557:12167000000]]
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@@ -1235,7 +1235,7 @@ class mwrank_MordellWeil(SageObject):
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WARNING: saturation at primes p > 3 will not be done;
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...
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Gained index 3
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- New regulator = 10.4285889689595992455
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+ New regulator = 10.42858...
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(False, 3, '[ ]')
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sage: EQ
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Subgroup of Mordell-Weil group: [[-2:3:1], [-14:25:8], [-13422227300:-49322830557:12167000000]]
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@@ -1249,7 +1249,7 @@ class mwrank_MordellWeil(SageObject):
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WARNING: saturation at primes p > 5 will not be done;
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...
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Gained index 5
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- New regulator = 0.417143558758383969818
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+ New regulator = 0.41714...
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(False, 5, '[ ]')
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sage: EQ
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Subgroup of Mordell-Weil group: [[-2:3:1], [-14:25:8], [1:-1:1]]
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diff --git a/src/sage/libs/eclib/mwrank.pyx b/src/sage/libs/eclib/mwrank.pyx
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index a4f89e1ca5..f8a22d2f55 100644
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--- a/src/sage/libs/eclib/mwrank.pyx
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+++ b/src/sage/libs/eclib/mwrank.pyx
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@@ -1234,9 +1234,9 @@ cdef class _two_descent:
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sage: D2.saturate()
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Searching for points (bound = 8)...done:
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found points which generate a subgroup of rank 3
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- and regulator 0.417143558758383969817119544618093396749810106098479
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+ and regulator 0.41714...
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Processing points found during 2-descent...done:
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- now regulator = 0.417143558758383969817119544618093396749810106098479
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+ now regulator = 0.41714...
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No saturation being done
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sage: D2.getbasis()
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'[[1:-1:1], [-2:3:1], [-14:25:8]]'
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@@ -1281,9 +1281,9 @@ cdef class _two_descent:
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sage: D2.saturate()
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Searching for points (bound = 8)...done:
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found points which generate a subgroup of rank 3
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- and regulator 0.417143558758383969817119544618093396749810106098479
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+ and regulator 0.41714...
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Processing points found during 2-descent...done:
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- now regulator = 0.417143558758383969817119544618093396749810106098479
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+ now regulator = 0.41714...
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No saturation being done
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sage: D2.getbasis()
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'[[1:-1:1], [-2:3:1], [-14:25:8]]'
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@@ -1329,9 +1329,9 @@ cdef class _two_descent:
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sage: D2.saturate()
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Searching for points (bound = 8)...done:
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found points which generate a subgroup of rank 3
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- and regulator 0.417143558758383969817119544618093396749810106098479
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+ and regulator 0.41714...
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Processing points found during 2-descent...done:
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- now regulator = 0.417143558758383969817119544618093396749810106098479
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+ now regulator = 0.41714...
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No saturation being done
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sage: D2.getbasis()
|
||||
'[[1:-1:1], [-2:3:1], [-14:25:8]]'
|
||||
|
|
@ -1,15 +0,0 @@
|
|||
diff --git a/build/pkgs/openblas/package-version.txt b/build/pkgs/openblas/package-version.txt
|
||||
index 3bc45c25d4..7c7c224887 100644
|
||||
--- a/src/sage/schemes/elliptic_curves/padics.py
|
||||
+++ b/src/sage/schemes/elliptic_curves/padics.py
|
||||
@@ -292,8 +292,8 @@ def padic_regulator(self, p, prec=20, height=None, check_hypotheses=True):
|
||||
|
||||
sage: max_prec = 30 # make sure we get past p^2 # long time
|
||||
sage: full = E.padic_regulator(5, max_prec) # long time
|
||||
- sage: for prec in range(1, max_prec): # long time
|
||||
- ....: assert E.padic_regulator(5, prec) == full # long time
|
||||
+ sage: for prec in range(1, max_prec): # known bug (#25969) # long time
|
||||
+ ....: assert E.padic_regulator(5, prec) == full # known bug (#25969) # long time
|
||||
|
||||
A case where the generator belongs to the formal group already
|
||||
(:trac:`3632`)::
|
||||
|
|
@ -1,12 +0,0 @@
|
|||
diff --git a/src/sage/all.py b/src/sage/all.py
|
||||
index 14cec431f1..25a35a0522 100644
|
||||
--- a/src/sage/all.py
|
||||
+++ b/src/sage/all.py
|
||||
@@ -310,6 +310,7 @@ warnings.filters.remove(('ignore', None, DeprecationWarning, None, 0))
|
||||
# Ignore all deprecations from IPython etc.
|
||||
warnings.filterwarnings('ignore',
|
||||
module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic)')
|
||||
+warnings.filterwarnings('ignore', "The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.") # matplotlib normed deprecation
|
||||
# However, be sure to keep OUR deprecation warnings
|
||||
warnings.filterwarnings('default',
|
||||
'[\s\S]*See http://trac.sagemath.org/[0-9]* for details.')
|
||||
|
|
@ -2,7 +2,6 @@
|
|||
, lib
|
||||
, writeTextFile
|
||||
, python
|
||||
, sage-src
|
||||
, sagelib
|
||||
, env-locations
|
||||
, gfortran
|
||||
|
|
@ -37,7 +36,7 @@
|
|||
, lcalc
|
||||
, rubiks
|
||||
, flintqs
|
||||
, openblas-cblas-pc
|
||||
, openblasCompat
|
||||
, flint
|
||||
, gmp
|
||||
, mpfr
|
||||
|
|
@ -47,6 +46,10 @@
|
|||
, ntl
|
||||
}:
|
||||
|
||||
# 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@"
|
||||
|
|
@ -96,26 +99,27 @@ writeTextFile rec {
|
|||
destination = "/${name}";
|
||||
text = ''
|
||||
export PKG_CONFIG_PATH='${lib.concatStringsSep ":" (map (pkg: "${pkg}/lib/pkgconfig") [
|
||||
# This is only needed in the src/sage/misc/cython.py test and I'm not sure if there's really a use-case
|
||||
# for it outside of the tests. However since singular and openblas are runtime dependencies anyways
|
||||
# and openblas-cblas-pc is tiny, it doesn't really hurt to include.
|
||||
# This is only needed in the src/sage/misc/cython.py test and I'm not
|
||||
# sure if there's really a usecase for it outside of the tests. However
|
||||
# since singular and openblas are runtime dependencies anyways, it doesn't
|
||||
# really hurt to include.
|
||||
singular
|
||||
openblas-cblas-pc
|
||||
openblasCompat
|
||||
])
|
||||
}'
|
||||
export SAGE_ROOT='${sage-src}'
|
||||
export SAGE_ROOT='${sagelib.src}'
|
||||
export SAGE_LOCAL='@sage-local@'
|
||||
export SAGE_SHARE='${sagelib}/share'
|
||||
orig_path="$PATH"
|
||||
export PATH='${runtimepath}'
|
||||
|
||||
# set dependent vars, like JUPYTER_CONFIG_DIR
|
||||
source "${sage-src}/src/bin/sage-env"
|
||||
source "${sagelib.src}/src/bin/sage-env"
|
||||
export PATH="${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:-${sage-src}/src/doc}"
|
||||
export SAGE_DOC_SRC="''${SAGE_DOC_SRC_OVERRIDE:-${sagelib.src}/src/doc}"
|
||||
|
||||
# set locations of dependencies
|
||||
. ${env-locations}/sage-env-locations
|
||||
|
|
@ -154,9 +158,11 @@ writeTextFile rec {
|
|||
|
||||
export SAGE_LIB='${sagelib}/${python.sitePackages}'
|
||||
|
||||
export SAGE_EXTCODE='${sage-src}/src/ext'
|
||||
export SAGE_EXTCODE='${sagelib.src}/src/ext'
|
||||
|
||||
# for find_library
|
||||
# for find_library
|
||||
export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}:$DYLD_LIBRARY_PATH"
|
||||
'';
|
||||
} // {
|
||||
lib = sagelib; # equivalent of `passthru`, which `writeTextFile` doesn't support
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,12 @@
|
|||
, fetchFromGitHub
|
||||
, fetchpatch
|
||||
}:
|
||||
|
||||
# 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 $out.
|
||||
# This is done because multiple derivations rely on these sources and they should
|
||||
# all get the same sources with the same patches applied.
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
version = "8.4";
|
||||
name = "sage-src-${version}";
|
||||
|
|
@ -13,6 +19,8 @@ stdenv.mkDerivation rec {
|
|||
sha256 = "0gips1hagiz9m7s21bg5as8hrrm2x5k47h1bsq0pc46iplfwmv2d";
|
||||
};
|
||||
|
||||
# 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 = [
|
||||
# https://trac.sagemath.org/ticket/25358
|
||||
(fetchpatch {
|
||||
|
|
@ -31,6 +39,7 @@ stdenv.mkDerivation rec {
|
|||
# Revert the commit that made the sphinx build fork even in the single thread
|
||||
# case. For some yet unknown reason, that breaks the docbuild on nix and archlinux.
|
||||
# See https://groups.google.com/forum/#!msg/sage-packaging/VU4h8IWGFLA/mrmCMocYBwAJ.
|
||||
# https://trac.sagemath.org/ticket/26608
|
||||
./patches/revert-sphinx-always-fork.patch
|
||||
|
||||
# Make sure py2/py3 tests are only run when their expected context (all "sage"
|
||||
|
|
@ -39,10 +48,16 @@ stdenv.mkDerivation rec {
|
|||
./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.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 = let
|
||||
# fetch a diff between base and rev on sage's git server
|
||||
# used to fetch trac tickets by setting the base to the release and the
|
||||
# revision to the last commit that should be included
|
||||
# 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.
|
||||
fetchSageDiff = { base, rev, ...}@args: (
|
||||
fetchpatch ({
|
||||
url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
|
||||
|
|
@ -54,7 +69,7 @@ stdenv.mkDerivation rec {
|
|||
in [
|
||||
# New glpk version has new warnings, filter those out until upstream sage has found a solution
|
||||
# https://trac.sagemath.org/ticket/24824
|
||||
./patches/pari-stackwarn.patch # not actually necessary since tha pari upgrade, but necessary for the glpk patch to apply
|
||||
./patches/pari-stackwarn.patch # not actually necessary since the pari upgrade, but necessary for the glpk patch to apply
|
||||
(fetchpatch {
|
||||
url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/dt-version-glpk-4.65-ignore-warnings.patch";
|
||||
sha256 = "0b9293v73wb4x13wv5zwyjgclc01zn16msccfzzi6znswklgvddp";
|
||||
|
|
@ -64,8 +79,8 @@ stdenv.mkDerivation rec {
|
|||
# https://trac.sagemath.org/ticket/25260
|
||||
./patches/numpy-1.15.1.patch
|
||||
|
||||
# ntl upgrade
|
||||
# https://trac.sagemath.org/ticket/25532#comment:29
|
||||
# needed for ntl update
|
||||
# https://trac.sagemath.org/ticket/25532
|
||||
(fetchpatch {
|
||||
name = "lcalc-c++11.patch";
|
||||
url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/sagemath-lcalc-c++11.patch?h=packages/sagemath&id=0e31ae526ab7c6b5c0bfacb3f8b1c4fd490035aa";
|
||||
|
|
@ -100,9 +115,7 @@ stdenv.mkDerivation rec {
|
|||
})
|
||||
];
|
||||
|
||||
patches = nixPatches ++ packageUpgradePatches ++ [
|
||||
./patches/known-padics-bug.patch
|
||||
];
|
||||
patches = nixPatches ++ packageUpgradePatches;
|
||||
|
||||
postPatch = ''
|
||||
# make sure shebangs etc are fixed, but sage-python23 still works
|
||||
|
|
|
|||
51
pkgs/applications/science/math/sage/sage-tests.nix
Normal file
51
pkgs/applications/science/math/sage/sage-tests.nix
Normal file
|
|
@ -0,0 +1,51 @@
|
|||
{ stdenv
|
||||
, lib
|
||||
, sage-with-env
|
||||
, makeWrapper
|
||||
, files ? null # "null" means run all tests
|
||||
, longTests ? true # run tests marked as "long time"
|
||||
}:
|
||||
|
||||
# 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 "";
|
||||
relpathToArg = relpath: lib.escapeShellArg "${src}/${relpath}"; # paths need to be absolute
|
||||
testFileList = lib.concatStringsSep " " (map relpathToArg files);
|
||||
in
|
||||
stdenv.mkDerivation rec {
|
||||
version = src.version;
|
||||
name = "sage-tests-${version}";
|
||||
inherit src;
|
||||
|
||||
buildInputs = [
|
||||
makeWrapper
|
||||
sage-with-env
|
||||
];
|
||||
|
||||
unpackPhase = "#do nothing";
|
||||
configurePhase = "#do nothing";
|
||||
buildPhase = "#do nothing";
|
||||
|
||||
installPhase = ''
|
||||
# This output is not actually needed for anything, the package just
|
||||
# exists to decouple the sage build from its t ests.
|
||||
|
||||
mkdir -p "$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 "$HOME"
|
||||
|
||||
# "--long" tests are in the order of 1h, without "--long" its 1/2h
|
||||
"sage" -t --nthreads "$NIX_BUILD_CORES" --optional=sage ${patienceSpecifier} ${testArgs}
|
||||
'';
|
||||
}
|
||||
|
|
@ -2,11 +2,7 @@
|
|||
, lib
|
||||
, makeWrapper
|
||||
, sage-env
|
||||
, sage-src
|
||||
, openblasCompat
|
||||
, openblas-blas-pc
|
||||
, openblas-cblas-pc
|
||||
, openblas-lapack-pc
|
||||
, pkg-config
|
||||
, three
|
||||
, singular
|
||||
|
|
@ -26,15 +22,15 @@
|
|||
, pythonEnv
|
||||
}:
|
||||
|
||||
# Wrapper that combined `sagelib` with `sage-env` to produce an actually
|
||||
# executable sage. No tests are run yet and no documentation is built.
|
||||
|
||||
let
|
||||
buildInputs = [
|
||||
pythonEnv # for patchShebangs
|
||||
makeWrapper
|
||||
pkg-config
|
||||
openblasCompat # lots of segfaults with regular (64 bit) openblas
|
||||
openblas-blas-pc
|
||||
openblas-cblas-pc
|
||||
openblas-lapack-pc
|
||||
singular
|
||||
three
|
||||
pynac
|
||||
|
|
@ -92,13 +88,12 @@ let
|
|||
input_names = map (dep: pkg_to_spkg_name dep patch_names) transitiveDeps;
|
||||
in
|
||||
stdenv.mkDerivation rec {
|
||||
version = sage-src.version;
|
||||
version = src.version;
|
||||
name = "sage-with-env-${version}";
|
||||
src = sage-env.lib.src;
|
||||
|
||||
inherit buildInputs;
|
||||
|
||||
src = sage-src;
|
||||
|
||||
configurePhase = "#do nothing";
|
||||
|
||||
buildPhase = ''
|
||||
|
|
@ -110,17 +105,24 @@ stdenv.mkDerivation rec {
|
|||
|
||||
installPhase = ''
|
||||
mkdir -p "$out/var/lib/sage"
|
||||
cp -r installed $out/var/lib/sage
|
||||
cp -r installed "$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 "$out/build/bin"
|
||||
|
||||
cp -f '${sage-env}/sage-env' "$out/bin/sage-env"
|
||||
substituteInPlace "$out/bin/sage-env" \
|
||||
--subst-var-by sage-local "$out"
|
||||
'';
|
||||
|
||||
passthru = {
|
||||
env = sage-env;
|
||||
};
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,41 +0,0 @@
|
|||
{ stdenv
|
||||
, makeWrapper
|
||||
, sage
|
||||
, sage-src
|
||||
, sagedoc
|
||||
, withDoc
|
||||
}:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
version = sage.version;
|
||||
name = "sage-${version}";
|
||||
|
||||
buildInputs = [
|
||||
makeWrapper
|
||||
];
|
||||
|
||||
unpackPhase = "#do nothing";
|
||||
configurePhase = "#do nothing";
|
||||
buildPhase = "#do nothing";
|
||||
|
||||
installPhase = ''
|
||||
mkdir -p "$out/bin"
|
||||
makeWrapper "${sage}/bin/sage" "$out/bin/sage" \
|
||||
--set SAGE_DOC_SRC_OVERRIDE "${sage-src}/src/doc" ${
|
||||
stdenv.lib.optionalString withDoc "--set SAGE_DOC_OVERRIDE ${sagedoc}/share/doc/sage"
|
||||
}
|
||||
'';
|
||||
|
||||
doInstallCheck = withDoc;
|
||||
installCheckPhase = ''
|
||||
export HOME="$TMPDIR/sage-home"
|
||||
mkdir -p "$HOME"
|
||||
"$out/bin/sage" -c 'browse_sage_doc._open("reference", testing=True)'
|
||||
'';
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab";
|
||||
license = licenses.gpl2;
|
||||
maintainers = with maintainers; [ timokau ];
|
||||
};
|
||||
}
|
||||
|
|
@ -1,14 +1,24 @@
|
|||
{ stdenv
|
||||
, sage-with-env
|
||||
, makeWrapper
|
||||
, sage-tests
|
||||
, sage-with-env
|
||||
, sagedoc
|
||||
, withDoc
|
||||
}:
|
||||
|
||||
# A wrapper that makes sure sage finds its docs (if they were build).
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
version = sage-with-env.version;
|
||||
name = "sage-tests-${version}";
|
||||
version = src.version;
|
||||
name = "sage-${version}";
|
||||
src = sage-with-env.env.lib.src;
|
||||
|
||||
buildInputs = [
|
||||
makeWrapper
|
||||
|
||||
# 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
|
||||
];
|
||||
|
||||
unpackPhase = "#do nothing";
|
||||
|
|
@ -17,16 +27,28 @@ stdenv.mkDerivation rec {
|
|||
|
||||
installPhase = ''
|
||||
mkdir -p "$out/bin"
|
||||
# Like a symlink, but make sure that $0 points to the original.
|
||||
makeWrapper "${sage-with-env}/bin/sage" "$out/bin/sage"
|
||||
makeWrapper "${sage-with-env}/bin/sage" "$out/bin/sage" \
|
||||
--set SAGE_DOC_SRC_OVERRIDE "${src}/src/doc" ${
|
||||
stdenv.lib.optionalString withDoc "--set SAGE_DOC_OVERRIDE ${sagedoc}/share/doc/sage"
|
||||
}
|
||||
'';
|
||||
|
||||
doInstallCheck = true;
|
||||
doInstallCheck = withDoc;
|
||||
installCheckPhase = ''
|
||||
export HOME="$TMPDIR/sage-home"
|
||||
mkdir -p "$HOME"
|
||||
|
||||
# "--long" tests are in the order of 1h, without "--long" its 1/2h
|
||||
"$out/bin/sage" -t --nthreads "$NIX_BUILD_CORES" --optional=sage --long --all
|
||||
"$out/bin/sage" -c 'browse_sage_doc._open("reference", testing=True)'
|
||||
'';
|
||||
|
||||
passthru = {
|
||||
tests = sage-tests;
|
||||
doc = sagedoc;
|
||||
lib = sage-with-env.env.lib;
|
||||
};
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab";
|
||||
license = licenses.gpl2;
|
||||
maintainers = with maintainers; [ timokau ];
|
||||
};
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,63 +1,49 @@
|
|||
{ stdenv
|
||||
, sage-src
|
||||
, sage-with-env
|
||||
, sagelib
|
||||
, python2
|
||||
, psutil
|
||||
, future
|
||||
, sphinx
|
||||
, sagenb
|
||||
, python
|
||||
, maxima-ecl
|
||||
, networkx
|
||||
, scipy
|
||||
, sympy
|
||||
, matplotlib
|
||||
, pillow
|
||||
, ipykernel
|
||||
, jupyter_client
|
||||
, tachyon
|
||||
, jmol
|
||||
, ipywidgets
|
||||
, typing
|
||||
, cddlib
|
||||
, pybrial
|
||||
}:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
version = sage-src.version;
|
||||
version = src.version;
|
||||
name = "sagedoc-${version}";
|
||||
src = sage-with-env.env.lib.src;
|
||||
|
||||
|
||||
# Building the documentation has many dependencies, because all documented
|
||||
# modules are imported and because matplotlib is used to produce plots.
|
||||
buildInputs = [
|
||||
sagelib
|
||||
python2
|
||||
sage-with-env.env.lib
|
||||
python
|
||||
maxima-ecl
|
||||
tachyon
|
||||
jmol
|
||||
cddlib
|
||||
] ++ (with python.pkgs; [
|
||||
psutil
|
||||
future
|
||||
sphinx
|
||||
sagenb
|
||||
maxima-ecl
|
||||
networkx
|
||||
scipy
|
||||
sympy
|
||||
matplotlib
|
||||
pillow
|
||||
networkx
|
||||
ipykernel
|
||||
jupyter_client
|
||||
tachyon
|
||||
jmol
|
||||
ipywidgets
|
||||
jupyter_client
|
||||
typing
|
||||
cddlib
|
||||
pybrial
|
||||
];
|
||||
]);
|
||||
|
||||
unpackPhase = ''
|
||||
export SAGE_DOC_OVERRIDE="$PWD/share/doc/sage"
|
||||
export SAGE_DOC_SRC_OVERRIDE="$PWD/docsrc"
|
||||
|
||||
cp -r "${sage-src}/src/doc" "$SAGE_DOC_SRC_OVERRIDE"
|
||||
cp -r "${src}/src/doc" "$SAGE_DOC_SRC_OVERRIDE"
|
||||
chmod -R 755 "$SAGE_DOC_SRC_OVERRIDE"
|
||||
'';
|
||||
|
||||
|
|
|
|||
|
|
@ -3,9 +3,6 @@
|
|||
, buildPythonPackage
|
||||
, arb
|
||||
, openblasCompat
|
||||
, openblas-blas-pc
|
||||
, openblas-cblas-pc
|
||||
, openblas-lapack-pc
|
||||
, brial
|
||||
, cliquer
|
||||
, cypari2
|
||||
|
|
@ -51,19 +48,20 @@
|
|||
, libbraiding
|
||||
}:
|
||||
|
||||
# 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 {
|
||||
format = "other";
|
||||
version = sage-src.version;
|
||||
pname = "sagelib";
|
||||
|
||||
version = src.version;
|
||||
name = "sagelib-${version}";
|
||||
src = sage-src;
|
||||
|
||||
nativeBuildInputs = [
|
||||
iml
|
||||
perl
|
||||
openblas-blas-pc
|
||||
openblas-cblas-pc
|
||||
openblas-lapack-pc
|
||||
jupyter_core
|
||||
];
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,3 @@
|
|||
# Has a cyclic dependency with sage (not expressed here) and is not useful outside of sage
|
||||
{ stdenv
|
||||
, fetchpatch
|
||||
, python
|
||||
|
|
@ -13,6 +12,10 @@
|
|||
, flask-babel
|
||||
}:
|
||||
|
||||
# Has a cyclic dependency with sage (not expressed here) and is not useful outside of sage.
|
||||
# Deprecated, hopefully soon to be removed. See
|
||||
# https://trac.sagemath.org/ticket/25837
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "sagenb";
|
||||
version = "2018-06-26"; # not 1.0.1 because of new flask syntax
|
||||
|
|
|
|||
|
|
@ -21358,9 +21358,7 @@ with pkgs;
|
|||
|
||||
scs = callPackage ../development/libraries/science/math/scs { };
|
||||
|
||||
sage = callPackage ../applications/science/math/sage {
|
||||
nixpkgs = pkgs;
|
||||
};
|
||||
sage = callPackage ../applications/science/math/sage { };
|
||||
sageWithDoc = sage.override { withDoc = true; };
|
||||
|
||||
suitesparse_4_2 = callPackage ../development/libraries/science/math/suitesparse/4.2.nix { };
|
||||
|
|
|
|||
Loading…
Reference in a new issue