diff options
Diffstat (limited to 'pkgs/applications/science/math/sage/default.nix')
| -rw-r--r-- | pkgs/applications/science/math/sage/default.nix | 423 |
1 files changed, 202 insertions, 221 deletions
diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 7f101bac147e..9ad112213ffd 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -1,230 +1,211 @@ -# TODO -# - consider writing a script to convert spkgs to nix packages, similar to vim -# or cabal2nix. This would allow a more efficient and "cleaner" build, greater -# flexibility and the possibility to select which dependencies to add and which -# to remove. It would also allow to use system packages for some dependencies -# and recompile others (optimized for the system) without recompiling everything. -# - add optdeps: -# - imagemagick -# - texlive full for documentation -# - ... -# - further seperate build outputs. Also maybe run `make doc`. -# Configure flags like --bindir and --libdir oculd also be used for that, see -# ./configure --help`. - -# Other resources: -# - https://wiki.debian.org/DebianScience/Sage -# - https://github.com/cschwan/sage-on-gentoo -# - https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath - -{ stdenv -, bash -, fetchurl -, perl -, gfortran6 -, python -, autoreconfHook -, gettext -, which -, texlive -, texinfo -, hevea -, buildDocs ? false -, optimize ? false # optimize sage to the current system (obviously impure) +{ nixpkgs +, withDoc ? false }: -stdenv.mkDerivation rec { - version = "8.1"; - name = "sage-${version}"; - - # Modified version of patchShebangs that patches to the sage-internal version if possible - # and falls back to the system version if not. - patchSageShebangs = ./patchSageShebangs.sh; - src = fetchurl { - # Note that the source is *not* fetched from github, since that doesn't - # the upstream folder with all the source tarballs of the spkgs. - # If those are not present they are fetched at build time, which breaks - # when building in a sandbox (and probably only works if you install the - # latest sage version). - urls = [ - "http://mirrors.mit.edu/sage/src/sage-${version}.tar.gz" - "ftp://ftp.fu-berlin.de/unix/misc/sage/src/sage-${version}.tar.gz" - "http://sagemath.polytechnic.edu.na/src/sage-${version}.tar.gz" - "ftp://ftp.sun.ac.za/pub/mirrors/www.sagemath.org/src/sage-${version}.tar.gz" - "http://sagemath.mirror.ac.za/src/sage-${version}.tar.gz" - "https://ftp.leg.uct.ac.za/pub/packages/sage/src/sage-${version}.tar.gz" - "http://mirror.ufs.ac.za/sagemath/src/sage-${version}.tar.gz" - "https://mirrors-usa.go-parts.com/sage/sagemath/src/sage-${version}.tar.gz" - "http://www.cecm.sfu.ca/sage/src/sage-${version}.tar.gz" - "http://files.sagemath.org/src/sage-${version}.tar.gz" - "https://mirrors.xmission.com/sage/src/sage-${version}.tar.gz" - "http://sagemath.c3sl.ufpr.br/src/sage-${version}.tar.gz" - "http://linorg.usp.br/sage/src/sage-${version}.tar.gz" - "http://mirror.hust.edu.cn/sagemath/src/sage-${version}.tar.gz" - "https://ftp.iitm.ac.in/sage/src/sage-${version}.tar.gz" - "http://ftp.kaist.ac.kr/sage/src/sage-${version}.tar.gz" - "https://ftp.riken.jp/sagemath/src/sage-${version}.tar.gz" - "https://mirrors.tuna.tsinghua.edu.cn/sagemath/src/sage-${version}.tar.gz" - "https://mirrors.ustc.edu.cn/sagemath/src/sage-${version}.tar.gz" - "http://ftp.tsukuba.wide.ad.jp/software/sage/src/sage-${version}.tar.gz" - "https://ftp.yz.yamagata-u.ac.jp/pub/math/sage/src/sage-${version}.tar.gz" - "https://mirror.yandex.ru/mirrors/sage.math.washington.edu/src/sage-${version}.tar.gz" - "https://mirror.aarnet.edu.au/pub/sage/src/sage-${version}.tar.gz" - "https://sage.mirror.garr.it/mirrors/sage/src/sage-${version}.tar.gz" - "https://www.mirrorservice.org/sites/www.sagemath.org/src/sage-${version}.tar.gz" - "http://mirror.switch.ch/mirror/sagemath/src/sage-${version}.tar.gz" - "https://mirrors.up.pt/pub/sage/src/sage-${version}.tar.gz" - "http://www-ftp.lip6.fr/pub/math/sagemath/src/sage-${version}.tar.gz" - "http://ftp.ntua.gr/pub/sagemath/src/sage-${version}.tar.gz" - ]; - sha256 = "1cpcs1mr0yii64s152xmxyd450bfzjb22jjj0zh9y3n6g9alzpyq"; +let + inherit (nixpkgs) fetchpatch fetchurl symlinkJoin fetchFromGitHub callPackage nodePackages_8_x; + + # https://trac.sagemath.org/ticket/15980 for tracking of python3 support + python = nixpkgs.python2.override { + packageOverrides = self: super: { + cypari2 = super.cypari2.override { inherit pari; }; + + cysignals = super.cysignals.override { inherit pari; }; + + cvxopt = super.cvxopt.override { inherit glpk; }; + + # https://github.com/sagemath/sagenb/issues/437 + flask-babel = super.flask-babel.overridePythonAttrs (attrs: rec { + version = "0.9"; + src = attrs.src.override { + inherit version; + sha256 = "0k7vk4k54y55ma0nx2k5s0phfqbriwslhy5shh3b0d046q7ibzaa"; + }; + doCheck = false; + }); + + # python packages that appear unmaintained and were not accepted into the nixpkgs + # tree because of that. These packages are only dependencies of the more-or-less + # deprecated sagenb. However sagenb is still a default dependency and the doctests + # depend on it. + # See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion. + flask-oldsessions = self.callPackage ./flask-oldsessions.nix {}; + flask-openid = self.callPackage ./flask-openid.nix {}; + python-openid = self.callPackage ./python-openid.nix {}; + + pybrial = self.callPackage ./pybrial.nix {}; + + sagelib = self.callPackage ./sagelib.nix { + inherit flint ecl pari glpk eclib; + inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular; + linbox = nixpkgs.linbox.override { withSage = true; }; + }; + + sagenb = self.callPackage ./sagenb.nix { + mathjax = nodePackages_8_x.mathjax; + }; + + sagedoc = self.callPackage ./sagedoc.nix { + inherit sage-src; + }; + + env-locations = self.callPackage ./env-locations.nix { + inherit pari_data ecl pari; + inherit singular; + three = nodePackages_8_x.three; + mathjax = nodePackages_8_x.mathjax; + }; + + sage-env = self.callPackage ./sage-env.nix { + inherit sage-src python rWrapper openblas-cblas-pc glpk ecl singular eclib pari palp flint pynac pythonEnv; + pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig + }; + + sage-with-env = self.callPackage ./sage-with-env.nix { + inherit pari eclib pythonEnv; + inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular; + pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig + three = nodePackages_8_x.three; + }; + + sage = self.callPackage ./sage.nix { }; + + sage-wrapper = self.callPackage ./sage-wrapper.nix { + inherit sage-src withDoc; + }; + }; }; - postPatch = '' - substituteAllInPlace src/bin/sage-env - bash=${bash} substituteAllInPlace build/bin/sage-spkg - ''; - - installPhase = '' - # Sage installs during first `make`, `make install` is no-op and just takes time. - ''; - - outputs = [ "out" ] ++ stdenv.lib.optionals (buildDocs) [ "doc" ]; - - buildInputs = [ - bash # needed for the build - perl # needed for the build - python # needed for the build - gfortran6 # needed to build giac, openblas - autoreconfHook # needed to configure sage with prefix - gettext # needed to build the singular spkg - which # needed in configure of mpir - texinfo # needed to build maxima - ] ++ stdenv.lib.optionals(buildDocs) [ - hevea # needed to build the docs of the giac spkg - (texlive.combine { inherit (texlive) - scheme-basic - collection-pstricks # needed by giac - times # font needed by giac - stmaryrd # needed by giac - babel-greek # optional for giac, otherwise throws a bunch of latex command not founds - ; - }) - ]; - - nativeBuildInputs = [ gfortran6 perl which ]; - - patches = [ - # fix usages of /bin/rm - ./spkg-singular.patch - # help python find the crypt library - # patches python3 and indirectly python2, since those installation files are symlinked - ./spkg-python.patch - # fix usages of /usr/bin/perl - ./spkg-git.patch - # fix usages of /bin/cp and add necessary argument to function call - ./spkg-giac.patch - # environment - ./env.patch - # adjust wrapper shebang and patch shebangs after each spkg build - ./shebangs.patch + openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; }; + openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; }; + openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; }; + + sage-src = callPackage ./sage-src.nix {}; + + pythonRuntimeDeps = with python.pkgs; [ + sagelib + pybrial + sagenb + cvxopt + networkx + service-identity + psutil + sympy + fpylll + matplotlib + scipy + ipywidgets + rpy2 + sphinx + typing + pillow ]; - enableParallelBuilding = true; + pythonEnv = python.buildEnv.override { + extraLibs = pythonRuntimeDeps; + ignoreCollisions = true; + } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible + + # needs to be rWrapper, standard "R" doesn't include default packages + rWrapper = nixpkgs.rWrapper.override { + # https://trac.sagemath.org/ticket/25674 + R = nixpkgs.R.overrideAttrs (attrs: rec { + name = "R-3.4.4"; + src = fetchurl { + url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz"; + sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"; + }; + }); + }; - hardeningDisable = [ - "format" # needed to build palp, for lines like `printf(ctime(&_NFL->TIME))` - # TODO could be patched with `sed s|printf(ctime(\(.*\)))|%s... or fixed upstream - ]; + # update causes issues + # https://groups.google.com/forum/#!topic/sage-packaging/cS3v05Q0zso + # https://trac.sagemath.org/ticket/24735 + singular = nixpkgs.singular.overrideAttrs (oldAttrs: { + name = "singular-4.1.0p3"; + src = fetchurl { + url = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/4-1-0/singular-4.1.0p3.tar.gz"; + sha256 = "105zs3zk46b1cps403ap9423rl48824ap5gyrdgmg8fma34680a4"; + }; + }); + + # *not* to confuse with the python package "pynac" + # https://trac.sagemath.org/ticket/24838 (depends on arb update) + pynac = nixpkgs.pynac.override { inherit singular; }; + + eclib = nixpkgs.eclib.override { inherit pari; }; + + # With openblas (64 bit), the tests fail the same way as when sage is build with + # openblas instead of openblasCompat. Apparently other packages somehow use flints + # blas when it is available. Alternative would be to override flint to use + # openblasCompat. + flint = nixpkgs.flint.override { withBlas = false; }; + + # Multiple palp dimensions need to be available and sage expects them all to be + # in the same folder. + palp = symlinkJoin { + name = "palp-${nixpkgs.palp.version}"; + paths = [ + (nixpkgs.palp.override { dimensions = 4; doSymlink = false; }) + (nixpkgs.palp.override { dimensions = 5; doSymlink = false; }) + (nixpkgs.palp.override { dimensions = 6; doSymlink = true; }) + (nixpkgs.palp.override { dimensions = 11; doSymlink = false; }) + ]; + }; - configureFlags = stdenv.lib.optionals(buildDocs) [ "--docdir=$(doc)" ]; - preConfigure = '' - export SAGE_NUM_THREADS="$NIX_BUILD_CORES" - - export HOME=/tmp/sage-home - export SAGE_ROOT="$PWD" - export SAGE_SRC="$PWD" - - mkdir -p "$HOME" - mkdir -p "$out" - - # we need to keep the source around - dir="$PWD" - cd .. - mv "$dir" "$out/sage-root" - - export SAGE_SPKG_INSTALL_DOCS='no' - cd "$out/sage-root" # build in target dir, since `make` is also `make install` - '' - + stdenv.lib.optionalString (buildDocs) '' - mkdir -p "$doc" - export SAGE_DOC="$doc" - export SAGE_DOCBUILD_OPTS="--no-pdf-links -k" - '' - + stdenv.lib.optionalString (!optimize) '' - export SAGE_FAT_BINARY=yes - ''; - - buildFlags = if (buildDocs) then "doc" else "build"; - - # for reference: http://doc.sagemath.org/html/en/installation/source.html - preBuild = '' - # symlink python to make sure the shebangs are patched to the sage path - # while still being able to use python before building it - # (this is important because otherwise sage will try to install python - # packages globally later on) - ln -s "${python}/bin/python2" $out/bin/python2 - ln -s "$out/bin/python2" $out/bin/python - touch $out/bin/python3 - bash $patchSageShebangs . - ''; - - postBuild = '' - # Clean up - rm -r "$out/sage-root/upstream" # don't keep the sources of all the spkgs - rm -rf "$out/sage-root/src/build" - rm -rf "$out/sage-root/src/autom4te.cache" - rm -rf "$out/sage-root/src/config" - rm -rf "$out/sage-root/src/m4" - rm -rf "$out/sage-root/.git" - rm -r "$out/sage-root/logs" - rm -r "$out"/lib/python*/test - # Fix dependency cycle between out and doc - rm -f "$out/sage-root/config.log" - rm -f "$out/sage-root/config.status" - rm -f "$out/sage-root/build/make/Makefile-auto" - rm -f "$out/sage-home/.sage/gap/libgap-workspace-"* - # Make sure unnessessary packages don't end up in the build closure - find "$out" \ - -iname 'config.log' \ - -delete \ - -or -iname 'Makefile' \ - -delete - rm -f "$out/lib/R/etc/Renviron" - # Make sure all shebangs are properly patched - bash $patchSageShebangs $out - ''; - - # TODO there are some doctest failures, which seem harmless. - # We should figure out a way to fix the failures or ignore only those tests. - doCheck = false; - - checkTarget = "ptestalllong"; # all long tests in parallell - preCheck = '' - export SAGE_TIMEOUT=0 # no timeout - export SAGE_TIMEOUT_LONG=0 # no timeout - ''; - - meta = { - homepage = http://www.sagemath.org; - description = "A free open source mathematics software system"; - # taken from the homepage - longDescription = '' - SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers. - Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab. - ''; - license = stdenv.lib.licenses.gpl2Plus; - platforms = ["x86_64-linux" "i686-linux"]; - maintainers = with stdenv.lib.maintainers; [ timokau ]; + # Sage expects those in the same directory. + pari_data = symlinkJoin { + name = "pari_data"; + paths = with nixpkgs; [ + pari-galdata + pari-seadata-small + ]; }; -} + + # https://trac.sagemath.org/ticket/22191 + ecl = nixpkgs.ecl_16_1_2; + + # sage currently uses an unreleased version of pari + pari = (nixpkgs.pari.override { withThread = false; }).overrideAttrs (attrs: rec { + version = "2.10-1280-g88fb5b3"; # on update remove pari-stackwarn patch from `sage-src.nix` + src = fetchurl { + url = "mirror://sageupstream/pari/pari-${version}.tar.gz"; + sha256 = "19gbsm8jqq3hraanbmsvzkbh88iwlqbckzbnga3y76r7k42akn7m"; + }; + }); + + # https://trac.sagemath.org/ticket/24824 + glpk = nixpkgs.glpk.overrideAttrs (attrs: rec { + version = "4.63"; + name = "glpk-${version}"; + src = fetchurl { + url = "mirror://gnu/glpk/${name}.tar.gz"; + sha256 = "1xp7nclmp8inp20968bvvfcwmz3mz03sbm0v3yjz8aqwlpqjfkci"; + }; + patches = (attrs.patches or []) ++ [ + # Alternatively patch sage with debians + # https://sources.debian.org/data/main/s/sagemath/8.1-7/debian/patches/t-version-glpk-4.60-extra-hack-fixes.patch + # The header of that debian patch contains a good description of the issue. The gist of it: + # > If GLPK in Sage causes one error, and this is caught by Sage and recovered from, then + # > later (because upstream GLPK does not clear the "error" flag) Sage will append + # > all subsequent terminal output of GLPK into the error_message string but not + # > actually forward it to the user's terminal. This breaks some doctests. + (fetchpatch { + name = "error_recovery.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/glpk/patches/error_recovery.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "0z99z9gd31apb6x5n5n26411qzx0ma3s6dnznc4x61x86bhq31qf"; + }) + + # Allow setting a exact verbosity level (OFF|ERR|ON|ALL|DBG) + (fetchpatch { + name = "exact_verbosity.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/glpk/patches/glp_exact_verbosity.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "15gm5i2alqla3m463i1qq6jx6c0ns6lip7njvbhp37pgxg4s9hx8"; + }) + ]; + }); +in + python.pkgs.sage-wrapper // { + doc = python.pkgs.sagedoc; + lib = python.pkgs.sagelib; + } |