diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/math/sage/sage-src.nix')
| -rw-r--r-- | nixpkgs/pkgs/applications/science/math/sage/sage-src.nix | 179 |
1 files changed, 179 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix new file mode 100644 index 000000000000..4791d12450a9 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix @@ -0,0 +1,179 @@ +{ stdenv +, fetchFromGitHub +, fetchpatch +, runtimeShell +}: + +# 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 = "8.9"; + pname = "sage-src"; + + src = fetchFromGitHub { + owner = "sagemath"; + repo = "sage"; + rev = version; + sha256 = "1bwga58x3s8z42w5h51c232f91ndsc1861dlb1glhax3pn0rhn3a"; + }; + + # 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 { + name = "safe-directory-test-without-patch.patch"; + url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=dc673c17555efca611f68398d5013b66e9825463"; + sha256 = "1hhannz7xzprijakn2w2d0rhd5zv2zikik9p51i87bas3nc658f7"; + }) + + # `is_unitary` test in `matrix_double_dense.pyx` fails with some BLAS implementations + # https://trac.sagemath.org/ticket/29297 should be included in 9.1 + (fetchpatch { + name = "is_unitary-special-case.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=cc3eb9ffa991e328b09028d32aab7e7cc2ddbb6a"; + sha256 = "0jq4w8hnp5c9q99011ldr4n3knvm1rx2g85z0hidv3i9x868p0ay"; + }) + + # Unfortunately inclusion in upstream sage was rejected. Instead the bug was + # fixed in python, but of course not backported to 2.7. So we'll probably + # have to keep this around until 2.7 is deprecated. + # https://trac.sagemath.org/ticket/25316 + # https://github.com/python/cpython/pull/7476 + ./patches/python-5755-hotpatch.patch + + # Make sure py2/py3 tests are only run when their expected context (all "sage" + # tests) are also run. That is necessary to test dochtml individually. See + # https://trac.sagemath.org/ticket/26110 for an upstream discussion. + ./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch + + # Fixes a potential race condition which can lead to transient doctest failures. + ./patches/fix-ecl-race.patch + + # Not necessary since library location is set explicitly + # https://trac.sagemath.org/ticket/27660#ticket + ./patches/do-not-test-find-library.patch + + # Parallelize docubuild using subprocesses, fixing an isolation issue. See + # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE + ./patches/sphinx-docbuild-subprocesses.patch + + # Fix doctest failures with docutils 0.15: + # https://nix-cache.s3.amazonaws.com/log/dzmzrb2zvardsmpy7idg7djkizmkzdhs-sage-tests-8.9.drv + # https://trac.sagemath.org/ticket/28856#comment:19 + ./patches/docutils-0.15.patch + ]; + + # Since sage unfortunately does not release bugfix releases, packagers must + # fix those bugs themselves. This is for critical bugfixes, where "critical" + # == "causes (transient) doctest failures / somebody complained". + bugfixPatches = [ + # To help debug the transient error in + # https://trac.sagemath.org/ticket/23087 when it next occurs. + ./patches/configurationpy-error-verbose.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 last release and the + # `rev` to the last commit of the ticket. + fetchSageDiff = { base, rev, name ? "sage-diff-${base}-${rev}.patch", ...}@args: ( + fetchpatch ({ + inherit name; + url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}"; + # We don't care about sage's own build system (which builds all its dependencies). + # Exclude build system changes to avoid conflicts. + excludes = [ "build/*" ]; + } // builtins.removeAttrs args [ "rev" "base" ]) + ); + in [ + # New glpk version has new warnings, filter those out until upstream sage has found a solution + # Should be fixed with glpk > 4.65. + # https://trac.sagemath.org/ticket/24824 + ./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"; + stripLen = 1; + }) + + # After updating smypow to (https://trac.sagemath.org/ticket/3360) we can + # now set the cache dir to be withing the .sage directory. This is not + # strictly necessary, but keeps us from littering in the user's HOME. + ./patches/sympow-cache.patch + + # https://trac.sagemath.org/ticket/28472 + (fetchpatch { + name = "eclib-20190909.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=d27dc479a5772d59e4bc85d805b6ffd595284f1d"; + sha256 = "1nf1s9y7n30lhlbdnam7sghgaq9nasmv96415gl5jlcf7a3hlxk3"; + }) + + # ignore a deprecation warning for usage of `cmp` in the attrs library in the doctests + ./patches/ignore-cmp-deprecation.patch + + # Werkzeug has deprecated ImmutableDict, but it is still used in legacy + # sagenb. That's no big issue since sagenb will be removed soon anyways. + ./patches/ignore-werkzeug-immutable-dict-deprecation.patch + + # threejs r109 (#28560) + (fetchpatch { + name = "threejs-r109.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=fcc11d6effa39f375bc5f4ea5831fb7a2f2767da"; + sha256 = "0hnmc8ld3bblks0hcjvjjaydkgwdr1cs3dbl2ys4gfq964pjgqwc"; + }) + + # https://trac.sagemath.org/ticket/28911 + (fetchpatch { + name = "sympy-1.5.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=c6d0308db15efd611211d26cfcbefbd180fc0831"; + sha256 = "0nwai2jr22h49km4hx3kwafs3mzsc5kwsv7mqwjf6ibwfx2bbgyq"; + }) + + # https://trac.sagemath.org/ticket/29313 (patch from ArchLinux) + (fetchpatch { + name = "pari-2.11.3.patch"; + url = "https://aur.archlinux.org/cgit/aur.git/plain/sagemath-pari-2.11.3.patch?h=sagemath-git&id=02e1d58bd1cd70935d69a4990469d18be6bd2c43"; + sha256 = "0z07444zvijyw96d11q7j81pvg7ysd6ycf1bbbjr6za9y74hv7d2"; + }) + ]; + + patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; + + postPatch = '' + # make sure shebangs etc are fixed, but sage-python23 still works + find . -type f -exec sed \ + -e 's/sage-python23/python/g' \ + -i {} \; + + echo '#!${runtimeShell} + python "$@"' > build/bin/sage-python23 + + # Make sure sage can at least be imported without setting any environment + # variables. It won't be close to feature complete though. + sed -i \ + "s|var('SAGE_LOCAL',.*|var('SAGE_LOCAL', '$out/src')|" \ + src/sage/env.py + + # Do not use sage-env-config (generated by ./configure). + # Instead variables are set manually. + echo '# do nothing' > src/bin/sage-env-config + ''; + + configurePhase = "# do nothing"; + + buildPhase = "# do nothing"; + + installPhase = '' + cp -r . "$out" + ''; +} |