diff options
Diffstat (limited to 'pkgs/applications/science/math/sage/sage-src.nix')
| -rw-r--r-- | pkgs/applications/science/math/sage/sage-src.nix | 197 |
1 files changed, 197 insertions, 0 deletions
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix new file mode 100644 index 000000000000..44b817944674 --- /dev/null +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -0,0 +1,197 @@ +{ stdenv +, fetchFromGitHub +, fetchpatch +}: +stdenv.mkDerivation rec { + version = "8.2"; + name = "sage-src-${version}"; + + src = fetchFromGitHub { + owner = "sagemath"; + repo = "sage"; + rev = version; + sha256 = "0d7vc16s7dj23an2cb8v5bhbnc6nsw20qhnnxr0xh8qg629027b8"; + }; + + nixPatches = [ + # https://trac.sagemath.org/ticket/25309 + (fetchpatch { + name = "spkg-paths.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=97f06fddee920399d4fcda65aa9b0925774aec69&id=a86151429ccce1ddd085e8090ada8ebdf02f3310"; + sha256 = "1xb9108rzzkdhn71vw44525620d3ww9jv1fph5a77v9y7nf9wgr7"; + }) + (fetchpatch { + name = "maxima-fas.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=97f06fddee920399d4fcda65aa9b0925774aec69"; + sha256 = "14s50yg3hpw9cp3v581dx7zfmpm2j972im7x30iwki8k45mjvk3i"; + }) + + # https://trac.sagemath.org/ticket/25328 + (fetchpatch { + name = "respect-jupyter-path.patch"; + url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=029123097d79f2c67bca2d725c470ef667a88ca2"; + sha256 = "0qw9p541ip0kn2gfvn4i05a06p50f3q46847gqfjjgzxhn62znfw"; + }) + + # 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"; + }) + + # https://trac.sagemath.org/ticket/25357 rebased on 8.2 + ./patches/python3-syntax-without-write.patch + + # https://trac.sagemath.org/ticket/25314 + (fetchpatch { + name = "make-qepcad-test-optional.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=fe294c58bd035ef427e268901d54a6faa0058138"; + sha256 = "003d5baf5c0n5rfg010ijwkwz8kg0s414cxwczs2vhdayxdixbix"; + }) + + # https://trac.sagemath.org/ticket/25316 + ./patches/python-5755-hotpatch.patch + + # https://trac.sagemath.org/ticket/25354 + # https://trac.sagemath.org/ticket/25531 + (fetchpatch { + name = "cysignals-include.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=28778bd25a37c80884d2b24e0683fb2989300cef"; + sha256 = "0fiiiw91pgs8avm9ggj8hb64bhqzl6jcw094d94nhirmh8w2jmc5"; + }) + + # https://trac.sagemath.org/ticket/25315 + (fetchpatch { + name = "find-libraries-in-dyld-library-path.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=20d4593876ce9c6004eac2ab6fd61786d0d96a06"; + sha256 = "1k3afq3qlzmgqwx6rzs5wv153vv9dsf5rk8pi61g57l3r3npbjmc"; + }) + + # Pari upstream has since accepted a patch, so this patch won't be necessary once sage updates pari. + # https://trac.sagemath.org/ticket/25312 + ./patches/pari-stackwarn.patch + + # https://trac.sagemath.org/ticket/25311 + ./patches/zn_poly_version.patch + + # https://trac.sagemath.org/ticket/25345 + # (upstream patch doesn't apply on 8.2 source) + ./patches/dochtml-optional.patch + ]; + + packageUpgradePatches = [ + # matplotlib 2.2.2 deprecated `normed` (replaced by `density`). + # This patch only ignores the warning. It would be equally easy to fix it + # (by replacing all mentions of `normed` by `density`), but its better to + # stay close to sage upstream. I didn't open an upstream ticket about it + # because the matplotlib update also requires a new dependency (kiwisolver) + # and I don't want to invest the time to learn how to add it. + ./patches/matplotlib-normed-deprecated.patch + + # Update to 20171219 broke the doctests because of insignificant precision + # changes, make the doctests less fragile. + # I didn't open an upstream ticket because its not entirely clear if + # 20171219 is really "released" yet. It is listed on the github releases + # page, but not marked as "latest release" and the homepage still links to + # the last version. + ./patches/eclib-regulator-precision.patch + + # sphinx 1.6 -> 1.7 upgrade + # https://trac.sagemath.org/ticket/24935 + ./patches/sphinx-1.7.patch + + # https://trac.sagemath.org/ticket/25320 + (fetchpatch { + name = "zero_division_error_formatting.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=f79070ddd09fa0ad6b340b097bd8d690a7aa35f0"; + sha256 = "02wsc3wbp8g8dk5jcjyv18d9v537h3zp5v8lwir46j4na4kj0dlb"; + }) + + # Adapt hashes to new boost version + # https://trac.sagemath.org/ticket/22243 + # (this ticket doesn't only upgrade boost but also avoids this problem in the future) + (fetchpatch { + name = "boost-upgrade.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=a24a9c6b30b93957333a3116196214a931325b69"; + sha256 = "0z3870g2ms2a81vnw08dc2i4k7jr62w8fggvcdwaavgd1wvdxwfl"; + }) + + # gfan 0.6.2 + # https://trac.sagemath.org/ticket/23353 + (fetchpatch { + name = "gfan-update.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=420215fc469cde733ec7a339e59b78ad6eec804c&id=112498a293ea2bf563e41aed35f1aa608f01b349"; + sha256 = "0ga3hkx8cr23dpc919lgvpi5lmy0d728jkq9z6kf0fl9s8g31mxb"; + }) + + # New glpk version has new warnings, filter those out until upstream sage has found a solution + # https://trac.sagemath.org/ticket/24824 + (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; + }) + + # https://trac.sagemath.org/ticket/25329 + (fetchpatch { + name = "dont-check-exact-glpk-version.patch"; + url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=89d068d8d77316bfffa6bf8e9ebf70b3b3b88e5c"; + sha256 = "00knwxs6fmymfgfl0q5kcavmxm9sf90a4r76y35n5s55gj8pl918"; + }) + + # https://trac.sagemath.org/ticket/25355 + (fetchpatch { + name = "maxima-5.41.0.patch"; + url = "https://git.sagemath.org/sage.git/patch/?id=87328023c4739abdf24108038201e3fa9bdfc739"; + sha256 = "0hxi7qr5mfx1bc32r8j7iba4gzd7c6v63asylyf5cbyp86azpb7i"; + }) + + # Update cddlib from 0.94g to 0.94h. + # https://trac.sagemath.org/ticket/25341 (doesn't apply to 8.2 sources) + (fetchpatch { + url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/u2-version-cddlib-094h.patch"; + sha256 = "0fmw7pzbaxs2dshky6iw9pr8i23p9ih2y2lw661qypdrxh5xw03k"; + stripLen = 1; + }) + ./patches/revert-269c1e1551285.patch + + + # Only formatting changes. + # https://trac.sagemath.org/ticket/25260 + ./patches/numpy-1.14.3.patch + + # https://trac.sagemath.org/ticket/24374 + (fetchpatch { + name = "networkx-2.1.patch"; + url = "https://salsa.debian.org/science-team/sagemath/raw/487df9ae48ca1d93d9b1cb3af8745d31e30fb741/debian/patches/u0-version-networkx-2.1.patch"; + sha256 = "1xxxawygbgxgvlv7b4w8hhzgdnva4rhmgdxaiaa3pwdwln0yc750"; + stripLen = 1; + }) + + ]; + + patches = nixPatches ++ 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 '#!${stdenv.shell} + python "$@"' > build/bin/sage-python23 + + # Do not use sage-env-config (generated by ./configure). + # Instead variables are set manually. + echo '# do nothing' > src/bin/sage-env-config + ''; + + configurePhase = "# do nothing"; + + buildPhase = "# do nothing"; + + installPhase = '' + cp -r . "$out" + ''; +} |