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We are migrating packages that meet below requirements: 1. using `callPackage` 2. called path is a directory 3. overriding set is empty (`{ }`) 4. not containing path expressions other than relative path (to makenixpkgs-vet happy) 5. not referenced by nix files outside of the directory, other than`pkgs/top-level/all-packages.nix` 6. not referencing nix files outside of the directory 7. not referencing `default.nix` (since it's changed to `package.nix`) 8. `outPath` doesn't change after migration The tool is here: https://github.com/Aleksanaa/by-name-migrate.
179 lines
5.8 KiB
Nix
179 lines
5.8 KiB
Nix
{ pkgs
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, withDoc ? false
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, requireSageTests ? true
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, extraPythonPackages ? ps: []
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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 (pkgs) symlinkJoin callPackage nodePackages;
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python3 = pkgs.python3 // {
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pkgs = pkgs.python3.pkgs.overrideScope (self: super: {
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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 flint3;
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inherit sage-src env-locations singular;
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inherit (maxima) lisp-compiler;
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linbox = pkgs.linbox;
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pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
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};
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sage-docbuild = self.callPackage ./python-modules/sage-docbuild.nix {
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inherit sage-src;
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};
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sage-setup = self.callPackage ./python-modules/sage-setup.nix {
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inherit sage-src;
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};
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});
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};
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# matches src/sage/repl/ipython_kernel/install.py:kernel_spec
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jupyter-kernel-definition = {
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displayName = "SageMath ${sage-src.version}";
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argv = [
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"${sage-with-env}/bin/sage" # FIXME which sage
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"--python"
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"-m"
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"sage.repl.ipython_kernel"
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"-f"
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"{connection_file}"
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];
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language = "sage";
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# just one 16x16 logo is available
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logo32 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png";
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logo64 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png";
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};
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jupyter-kernel-specs = pkgs.jupyter-kernel.create {
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definitions = pkgs.jupyter-kernel.default // {
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sagemath = jupyter-kernel-definition;
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};
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};
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three = callPackage ./threejs-sage.nix { };
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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;
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inherit singular maxima;
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inherit three;
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cysignals = python3.pkgs.cysignals;
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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 = python3.pkgs.sagelib;
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sage-docbuild = python3.pkgs.sage-docbuild;
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inherit env-locations;
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inherit python3 singular palp flint3 pythonEnv maxima;
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pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
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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 jupyter-kernel-specs;
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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 python3 pythonEnv;
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inherit sage-env;
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inherit singular maxima;
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inherit three;
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pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
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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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pytest = python3.pkgs.pytest;
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};
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sage-src = callPackage ./sage-src.nix {};
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pythonRuntimeDeps = with python3.pkgs; [
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sagelib
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sage-docbuild
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cvxopt
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networkx
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service-identity
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psutil
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sympy
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fpylll
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matplotlib
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tkinter # optional, as a matplotlib backend (use with `%matplotlib tk`)
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scipy
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ipywidgets
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notebook # for "sage -n"
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rpy2
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sphinx
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pillow
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] ++ extraPythonPackages python3.pkgs;
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pythonEnv = python3.buildEnv.override {
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extraLibs = pythonRuntimeDeps;
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ignoreCollisions = true;
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} // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
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singular = pkgs.singular.override { inherit flint3; };
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maxima = pkgs.maxima-ecl.override {
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lisp-compiler = pkgs.ecl.override {
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# "echo syntax error | ecl > /dev/full 2>&1" segfaults in
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# ECL. We apply a patch to fix it (write_error.patch), but it
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# only works if threads are disabled. sage 9.2 tests this
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# (src/sage/interfaces/tests.py) and ships ecl like so.
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# https://gitlab.com/embeddable-common-lisp/ecl/-/merge_requests/1#note_1657275
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threadSupport = false;
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# if we don't use the system boehmgc, sending a SIGINT to ecl
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# can segfault if we it happens during memory allocation.
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# src/sage/libs/ecl.pyx would intermittently fail in this case.
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useBoehmgc = true;
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};
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};
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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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flint3 = pkgs.flint3.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-${pkgs.palp.version}";
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paths = [
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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 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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in
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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 jupyter-kernel-definition jupyter-kernel-specs;
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inherit withDoc requireSageTests;
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}
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