179 lines
7.5 KiB
Nix
179 lines
7.5 KiB
Nix
{ stdenv
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, fetchFromGitHub
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, fetchpatch
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, runtimeShell
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}:
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# This file is responsible for fetching the sage source and adding necessary patches.
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# It does not actually build anything, it just copies the patched sources to $out.
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# This is done because multiple derivations rely on these sources and they should
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# all get the same sources with the same patches applied.
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stdenv.mkDerivation rec {
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version = "8.9";
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pname = "sage-src";
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src = fetchFromGitHub {
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owner = "sagemath";
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repo = "sage";
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rev = version;
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sha256 = "1bwga58x3s8z42w5h51c232f91ndsc1861dlb1glhax3pn0rhn3a";
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};
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# Patches needed because of particularities of nix or the way this is packaged.
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# The goal is to upstream all of them and get rid of this list.
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nixPatches = [
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# https://trac.sagemath.org/ticket/25358
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(fetchpatch {
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name = "safe-directory-test-without-patch.patch";
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url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=dc673c17555efca611f68398d5013b66e9825463";
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sha256 = "1hhannz7xzprijakn2w2d0rhd5zv2zikik9p51i87bas3nc658f7";
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})
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# `is_unitary` test in `matrix_double_dense.pyx` fails with some BLAS implementations
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# https://trac.sagemath.org/ticket/29297 should be included in 9.1
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(fetchpatch {
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name = "is_unitary-special-case.patch";
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url = "https://git.sagemath.org/sage.git/patch?id=cc3eb9ffa991e328b09028d32aab7e7cc2ddbb6a";
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sha256 = "0jq4w8hnp5c9q99011ldr4n3knvm1rx2g85z0hidv3i9x868p0ay";
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})
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# Unfortunately inclusion in upstream sage was rejected. Instead the bug was
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# fixed in python, but of course not backported to 2.7. So we'll probably
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# have to keep this around until 2.7 is deprecated.
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# https://trac.sagemath.org/ticket/25316
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# https://github.com/python/cpython/pull/7476
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./patches/python-5755-hotpatch.patch
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# Make sure py2/py3 tests are only run when their expected context (all "sage"
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# tests) are also run. That is necessary to test dochtml individually. See
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# https://trac.sagemath.org/ticket/26110 for an upstream discussion.
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./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch
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# Fixes a potential race condition which can lead to transient doctest failures.
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./patches/fix-ecl-race.patch
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# Not necessary since library location is set explicitly
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# https://trac.sagemath.org/ticket/27660#ticket
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./patches/do-not-test-find-library.patch
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# Parallelize docubuild using subprocesses, fixing an isolation issue. See
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# https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
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./patches/sphinx-docbuild-subprocesses.patch
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# Fix doctest failures with docutils 0.15:
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# https://nix-cache.s3.amazonaws.com/log/dzmzrb2zvardsmpy7idg7djkizmkzdhs-sage-tests-8.9.drv
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# https://trac.sagemath.org/ticket/28856#comment:19
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./patches/docutils-0.15.patch
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];
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# Since sage unfortunately does not release bugfix releases, packagers must
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# fix those bugs themselves. This is for critical bugfixes, where "critical"
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# == "causes (transient) doctest failures / somebody complained".
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bugfixPatches = [
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# To help debug the transient error in
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# https://trac.sagemath.org/ticket/23087 when it next occurs.
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./patches/configurationpy-error-verbose.patch
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];
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# Patches needed because of package updates. We could just pin the versions of
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# dependencies, but that would lead to rebuilds, confusion and the burdons of
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# maintaining multiple versions of dependencies. Instead we try to make sage
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# compatible with never dependency versions when possible. All these changes
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# should come from or be proposed to upstream. This list will probably never
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# be empty since dependencies update all the time.
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packageUpgradePatches = let
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# Fetch a diff between `base` and `rev` on sage's git server.
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# Used to fetch trac tickets by setting the `base` to the last release and the
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# `rev` to the last commit of the ticket.
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fetchSageDiff = { base, rev, name ? "sage-diff-${base}-${rev}.patch", ...}@args: (
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fetchpatch ({
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inherit name;
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url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
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# We don't care about sage's own build system (which builds all its dependencies).
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# Exclude build system changes to avoid conflicts.
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excludes = [ "build/*" ];
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} // builtins.removeAttrs args [ "rev" "base" ])
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);
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in [
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# New glpk version has new warnings, filter those out until upstream sage has found a solution
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# Should be fixed with glpk > 4.65.
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# https://trac.sagemath.org/ticket/24824
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./patches/pari-stackwarn.patch # not actually necessary since the pari upgrade, but necessary for the glpk patch to apply
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(fetchpatch {
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url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/dt-version-glpk-4.65-ignore-warnings.patch";
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sha256 = "0b9293v73wb4x13wv5zwyjgclc01zn16msccfzzi6znswklgvddp";
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stripLen = 1;
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})
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# After updating smypow to (https://trac.sagemath.org/ticket/3360) we can
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# now set the cache dir to be withing the .sage directory. This is not
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# strictly necessary, but keeps us from littering in the user's HOME.
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./patches/sympow-cache.patch
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# https://trac.sagemath.org/ticket/28472
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(fetchpatch {
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name = "eclib-20190909.patch";
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url = "https://git.sagemath.org/sage.git/patch?id=d27dc479a5772d59e4bc85d805b6ffd595284f1d";
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sha256 = "1nf1s9y7n30lhlbdnam7sghgaq9nasmv96415gl5jlcf7a3hlxk3";
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})
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# ignore a deprecation warning for usage of `cmp` in the attrs library in the doctests
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./patches/ignore-cmp-deprecation.patch
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# Werkzeug has deprecated ImmutableDict, but it is still used in legacy
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# sagenb. That's no big issue since sagenb will be removed soon anyways.
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./patches/ignore-werkzeug-immutable-dict-deprecation.patch
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# threejs r109 (#28560)
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(fetchpatch {
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name = "threejs-r109.patch";
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url = "https://git.sagemath.org/sage.git/patch?id=fcc11d6effa39f375bc5f4ea5831fb7a2f2767da";
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sha256 = "0hnmc8ld3bblks0hcjvjjaydkgwdr1cs3dbl2ys4gfq964pjgqwc";
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})
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# https://trac.sagemath.org/ticket/28911
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(fetchpatch {
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name = "sympy-1.5.patch";
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url = "https://git.sagemath.org/sage.git/patch/?h=c6d0308db15efd611211d26cfcbefbd180fc0831";
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sha256 = "0nwai2jr22h49km4hx3kwafs3mzsc5kwsv7mqwjf6ibwfx2bbgyq";
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})
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# https://trac.sagemath.org/ticket/29313 (patch from ArchLinux)
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(fetchpatch {
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name = "pari-2.11.3.patch";
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url = "https://aur.archlinux.org/cgit/aur.git/plain/sagemath-pari-2.11.3.patch?h=sagemath-git&id=02e1d58bd1cd70935d69a4990469d18be6bd2c43";
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sha256 = "0z07444zvijyw96d11q7j81pvg7ysd6ycf1bbbjr6za9y74hv7d2";
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})
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];
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patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;
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postPatch = ''
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# make sure shebangs etc are fixed, but sage-python23 still works
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find . -type f -exec sed \
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-e 's/sage-python23/python/g' \
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-i {} \;
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echo '#!${runtimeShell}
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python "$@"' > build/bin/sage-python23
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# Make sure sage can at least be imported without setting any environment
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# variables. It won't be close to feature complete though.
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sed -i \
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"s|var('SAGE_LOCAL',.*|var('SAGE_LOCAL', '$out/src')|" \
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src/sage/env.py
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# Do not use sage-env-config (generated by ./configure).
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# Instead variables are set manually.
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echo '# do nothing' > src/bin/sage-env-config
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'';
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configurePhase = "# do nothing";
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buildPhase = "# do nothing";
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installPhase = ''
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cp -r . "$out"
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'';
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}
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