diff --git a/pkgs/applications/science/math/sage/README.md b/pkgs/applications/science/math/sage/README.md new file mode 100644 index 000000000000..46496664f28e --- /dev/null +++ b/pkgs/applications/science/math/sage/README.md @@ -0,0 +1,117 @@ +# Sage on nixos + +Sage is a pretty complex package that depends on many other complex packages and patches some of those. As a result, the sage nix package is also quite complex. + +Don't feel discouraged to fix, simplify or improve things though. Here's a quick overview over the functions of the individual files: + +- `sage-src.nix` + Downloads the source code and applies patches. This makes sure that all the other files work with the same sage source. If you want to apply a patch to sage or update sage to a new version, this is the place to do it. + +- `env-locations.nix` + Creates a bash file that sets a bunch of environment variables telling sage where to find various packages and files. The definitions of those environment variables can be found in the sage source in the `src/env.py` file. This bash file needs to be sourced before sage is started (done in `sage-env.nix` and `sagedoc.nix`). + +- `sage-env.nix` + Sets all environment variables sage needs to run. This includes the package locations defined in `env-locations.nix` as well as the location of sage itself and its various subdirectories. + +- `sagelib.nix` + Defines the main sage package (without setting the necessary environments or running any tests). + +- `sage-with-env.nix` + Wraps sage in the necessary environment. + +- `sage.nix` + Runs sages doctests. + +- `sage-wrapper.nix` + Optionally tells sage where do find the docs. + +- `sagedoc.nix` + Builds and tests the sage html documentation. Can be used for offline documentation viewing as well as the sage `browse_sage_doc` and `search_doc` functions. + +- `sagenb.nix` + The (semi deprecated) sage notebook. + +- `default.nix` + Introduces necessary overrides, defines new packages and ties everything together (returning the `sage` package). + +- `flask-oldsessions.nix`, `flask-openid.nix`, `python-openid.nix` + These are python packages that were rejected from the main nixpkgs tree because they appear unmaintained. They are needed for the (semi-deprecated) sage notebook. Since that notebook is still needed to run the sage doctests, these packages are included but not exposed to the rest of nixpkgs. + +- `pybrial.nix` + pybrial is a dependency of sage. However, pybrial itself also has sage as a dependency. Because of that circular dependency, pybrial is hidden from the rest of nixpkgs (just as the flask packages and python-openid. + +- `openblas-pc.nix` + This creates a `.pc` file to be read by `pkg-config` that allows openblas to take on different roles, like `cblas` or `lapack`. + +## The sage build is broken + +First you should find out which change to nixpkgs is at fault (if you don't already know). You can use `git-bisect` for that (see the manpage). + +If the build broke as a result of a package update, try those solutions in order: + +- search the [sage trac](https://trac.sagemath.org/) for keywords like "Upgrade ". Maybe somebody has already proposed a patch that fixes the issue. You can then add a `fetchpatch` to `sage-src.nix`. + +- check if [gentoo](https://github.com/cschwan/sage-on-gentoo/tree/master/sci-mathematics/sage), [debian](https://salsa.debian.org/science-team/sagemath/tree/master/debian) or [arch linux](https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath) already solved the problem. You can then again add a `fetchpatch` to `sage-src.nix`. If applicable you should also [propose the patch upstream](#proposing-a-sage-patch). + +- fix the problem yourself. First clone the sagemath source and then check out the sage version you want to patch: + +``` +[user@localhost ~]$ git clone git://github.com/sagemath/sage.git +[user@localhost ~]$ cd sage +[user@localhost sage]$ git checkout 8.2 # substitute the relevant version here +``` + +Then make the needed changes and generate a patch with `git diff`: + +``` +[user@localhost ~]$ +[user@localhost ~]$ git diff -u > /path/to/nixpkgs/pkgs/applications/science/math/sage/patches/name-of-patch.patch +``` + +Now just add the patch to `sage-src.nix` and test your changes. If they fix the problem, [propose them upstream](#proposing-a-sage-patch) and add a link to the trac ticket. + +- pin the package version in `default.nix` and add a note that explains why that is necessary. + + +## Proposing a sage patch + +You can [login the sage trac using GitHub](https://trac.sagemath.org/login). Your username will then be `gh-`. The only other way is to request a trac account via email. After that refer to [git the hard way](http://doc.sagemath.org/html/en/developer/manual_git.html#chapter-manual-git) in the sage documentation. The "easy way" requires a non-GitHub account (requested via email) and a special tool. The "hard way" is really not all that hard if you're a bit familiar with git. + +Here's the gist, assuming you want to use ssh key authentication. First, [add your public ssh key](https://trac.sagemath.org/prefs/sshkeys). Then: + +``` +[user@localhost ~]$ git clone git://github.com/sagemath/sage.git +[user@localhost ~]$ cd sage +[user@localhost sage]$ git remote add trac git@trac.sagemath.org:sage.git -t master +[user@localhost sage]$ git checkout -b u/gh-/ develop +[user@localhost sage]$ +[user@localhost sage]$ git add . +[user@localhost sage]$ git commit +[user@localhost sage]$ git show # review your changes +[user@localhost sage]$ git push --set-upstream trac u/gh-/ +``` + +You now created a branch on the trac server (you *must* follow the naming scheme as you only have push access to branches with the `u/gh-/` prefix). +Now you can [create a new trac ticket](https://trac.sagemath.org/newticket). +- Write a description of the change +- set the type and component as appropriate +- write your real name in the "Authors" field +- write `u/gh-/` in the "Branch" field +- click "Create ticket" +- click "Modify" on the top right of your ticket (for some reason you can only change the ticket status after you have created it) +- set the ticket status from `new` to `needs_review` +- click "Save changes" + +Refer to sages [Developer's Guide](http://doc.sagemath.org/html/en/developer/index.html) for further details. + +## I want to update sage + +You'll need to change the `version` field in `sage-src.nix`. Afterwards just try to build and let nix tell you which patches no longer apply (hopefully because they were adopted upstream). Remove those. + +Hopefully the build will succeed now. If it doesn't and the problem is obvious, fix it as described in [The sage build is broken](#the-sage-build-is-broken). +If the problem is not obvious, you can try to first update sage to an intermediate version (remember that you can also set the `version` field to any git revision of sage) and locate the sage commit that introduced the issue. You can even use `git-bisect` for that (it will only be a bit tricky to keep track of which patches to apply). Hopefully after that the issue will be obvious. + +## Well, that didn't help! + +If you couldn't fix the problem, create a GitHub issue on the nixpkgs repo and ping @timokau (or whoever is listed in the `maintainers` list of the sage package). +Describe what you did and why it didn't work. Afterwards it would be great if you help the next guy out and improve this documentation! 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-${version}"; +let + inherit (nixpkgs) fetchpatch fetchurl symlinkJoin fetchFromGitHub callPackage nodePackages_8_x; - # Modified version of patchShebangs that patches to the sage-internal version if possible - # and falls back to the system version if not. - patchSageShebangs = ./patchSageShebangs.sh; - src = fetchurl { - # Note that the source is *not* fetched from github, since that doesn't - # the upstream folder with all the source tarballs of the spkgs. - # If those are not present they are fetched at build time, which breaks - # when building in a sandbox (and probably only works if you install the - # latest sage version). - urls = [ - "http://mirrors.mit.edu/sage/src/sage-${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" + # 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; + }; + }; + }; + + 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 + ]; + + 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/${name}.tar.gz"; + sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"; + }; + }); + }; + + # update causes issues + # https://groups.google.com/forum/#!topic/sage-packaging/cS3v05Q0zso + # https://trac.sagemath.org/ticket/24735 + singular = nixpkgs.singular.overrideAttrs (oldAttrs: { + name = "singular-4.1.0p3"; + src = fetchurl { + url = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/4-1-0/singular-4.1.0p3.tar.gz"; + sha256 = "105zs3zk46b1cps403ap9423rl48824ap5gyrdgmg8fma34680a4"; + }; + }); + + # *not* to confuse with the python package "pynac" + # https://trac.sagemath.org/ticket/24838 (depends on arb update) + pynac = nixpkgs.pynac.override { inherit singular; }; + + eclib = nixpkgs.eclib.override { inherit pari; }; + + # With openblas (64 bit), the tests fail the same way as when sage is build with + # openblas instead of openblasCompat. Apparently other packages somehow use flints + # blas when it is available. Alternative would be to override flint to use + # openblasCompat. + flint = nixpkgs.flint.override { withBlas = false; }; + + # Multiple palp dimensions need to be available and sage expects them all to be + # in the same folder. + palp = symlinkJoin { + name = "palp-${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; }) ]; - sha256 = "1cpcs1mr0yii64s152xmxyd450bfzjb22jjj0zh9y3n6g9alzpyq"; }; - 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 - ]; - - enableParallelBuilding = true; - - 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 - ]; - - 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; + } diff --git a/pkgs/applications/science/math/sage/env-locations.nix b/pkgs/applications/science/math/sage/env-locations.nix new file mode 100644 index 000000000000..2ed079ab32bc --- /dev/null +++ b/pkgs/applications/science/math/sage/env-locations.nix @@ -0,0 +1,46 @@ +{ stdenv +, writeTextFile +, pari_data +, pari +, singular +, maxima-ecl +, conway_polynomials +, graphs +, elliptic_curves +, polytopes_db +, gap-libgap-compatible +, ecl +, combinatorial_designs +, jmol +, mathjax +, three +, cysignals +}: + +writeTextFile rec { + name = "sage-env-locations"; + destination = "/${name}"; + text = '' + export GP_DATA_DIR="${pari_data}/share/pari" + export PARI_DATA_DIR="${pari_data}" + export GPHELP="${pari}/bin/gphelp" + export GPDOCDIR="${pari}/share/pari/doc" + export SINGULARPATH='${singular}/share/singular' + export SINGULAR_SO='${singular}/lib/libSingular.so' + export SINGULAR_EXECUTABLE='${singular}/bin/Singular' + export MAXIMA_FAS='${maxima-ecl}/lib/maxima/${maxima-ecl.version}/binary-ecl/maxima.fas' + export MAXIMA_PREFIX="${maxima-ecl}" + export CONWAY_POLYNOMIALS_DATA_DIR='${conway_polynomials}/share/conway_polynomials' + export GRAPHS_DATA_DIR='${graphs}/share/graphs' + export ELLCURVE_DATA_DIR='${elliptic_curves}/share/ellcurves' + export POLYTOPE_DATA_DIR='${polytopes_db}/share/reflexive_polytopes' + export GAP_ROOT_DIR='${gap-libgap-compatible}/share/gap/build-dir' + export ECLDIR='${ecl}/lib/ecl-${ecl.version}/' + export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs" + export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona" + export JMOL_DIR="${jmol}" + export MATHJAX_DIR="${mathjax}/lib/node_modules/mathjax" + export THREEJS_DIR="${three}/lib/node_modules/three" + export SAGE_INCLUDE_DIRECTORIES="${cysignals}/lib/python2.7/site-packages" + ''; +} diff --git a/pkgs/applications/science/math/sage/env.patch b/pkgs/applications/science/math/sage/env.patch deleted file mode 100644 index a7f8538eac3d..000000000000 --- a/pkgs/applications/science/math/sage/env.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/src/bin/sage-env b/src/bin/sage-env -index ead308f861..ed8db9f9b7 100644 ---- a/src/bin/sage-env -+++ b/src/bin/sage-env -@@ -111,6 +111,8 @@ resolvelinks() { - } - - -+SAGE_ROOT="@out@/sage-root" -+ - # New value for SAGE_ROOT: either SAGE_ROOT (if given) - # or a guessed value based on pwd. - if [ -n "$SAGE_ROOT" ]; then -@@ -185,6 +187,8 @@ fi - export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION - - export SAGE_ROOT="$NEW_SAGE_ROOT" -+export SAGE_LOCAL='@out@/' -+export PYTHONPATH="@out@/lib/python2.7/site-packages:$PYTHONPATH" - - - # sage-env must know where the Sage's script files are. diff --git a/pkgs/applications/science/math/sage/fetch-mirrors.sh b/pkgs/applications/science/math/sage/fetch-mirrors.sh deleted file mode 100755 index a1103e86beb9..000000000000 --- a/pkgs/applications/science/math/sage/fetch-mirrors.sh +++ /dev/null @@ -1,11 +0,0 @@ -#! /usr/bin/env nix-shell -#! nix-shell -i bash -p curl go-pup - -# Fetches a list of all available source mirrors from the sage homepage. -# Note that the list is sorted by country, but fetchurl doesn't offer an option -# to customize mirror preference. - -curl -s http://www.sagemath.org/download-source.html \ - | pup 'table#mirror' \ - | pup 'a attr{href}' \ - | sed -e 's/index\.html/sage-${version}.tar.gz/' diff --git a/pkgs/applications/science/math/sage/flask-oldsessions.nix b/pkgs/applications/science/math/sage/flask-oldsessions.nix new file mode 100644 index 000000000000..85e35736d030 --- /dev/null +++ b/pkgs/applications/science/math/sage/flask-oldsessions.nix @@ -0,0 +1,36 @@ +{ stdenv +, buildPythonPackage +, fetchFromGitHub +, python +, flask +}: + +buildPythonPackage rec { + pname = "Flask-OldSessions"; + version = "0.10"; + + # no artifact on pypi: https://github.com/mitsuhiko/flask-oldsessions/issues/1 + src = fetchFromGitHub { + owner = "mitsuhiko"; + repo = "flask-oldsessions"; + rev = "${version}"; + sha256 = "04b5m8njjiwld9a0zw55iqwvyjgwcpdbhz1cic8nyhgcmypbicqn"; + }; + + propagatedBuildInputs = [ + flask + ]; + + # missing module flask.testsuite, probably assumes an old version of flask + doCheck = false; + checkPhase = '' + ${python.interpreter} run-tests.py + ''; + + meta = with stdenv.lib; { + description = "Provides a session class that works like the one in Flask before 0.10."; + license = licenses.bsd2; + maintainers = with maintainers; [ timokau ]; + homepage = https://github.com/mitsuhiko/flask-oldsessions; + }; +} diff --git a/pkgs/applications/science/math/sage/flask-openid.nix b/pkgs/applications/science/math/sage/flask-openid.nix new file mode 100644 index 000000000000..9043fabd9b4a --- /dev/null +++ b/pkgs/applications/science/math/sage/flask-openid.nix @@ -0,0 +1,28 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, flask +, python-openid +}: + +buildPythonPackage rec { + pname = "Flask-OpenID"; + version = "1.2.5"; + + src = fetchPypi { + inherit pname version; + sha256 = "1aycwmwi7ilcaa5ab8hm0bp6323zl8z25q9ha0gwrl8aihfgx3ss"; + }; + + propagatedBuildInputs = [ + flask + python-openid + ]; + + meta = with stdenv.lib; { + description = "Adds openid support to flask applications"; + license = licenses.bsd2; + maintainers = with maintainers; [ timokau ]; + homepage = https://pythonhosted.org/Flask-OpenID/; + }; +} diff --git a/pkgs/applications/science/math/sage/openblas-pc.nix b/pkgs/applications/science/math/sage/openblas-pc.nix new file mode 100644 index 000000000000..ba46850bbc61 --- /dev/null +++ b/pkgs/applications/science/math/sage/openblas-pc.nix @@ -0,0 +1,18 @@ +{ stdenv +, openblasCompat +, writeTextFile +, name +}: + +writeTextFile { + name = "openblas-${name}-pc-${openblasCompat.version}"; + destination = "/lib/pkgconfig/${name}.pc"; + text = '' + Name: ${name} + Version: ${openblasCompat.version} + + Description: ${name} for SageMath, provided by the OpenBLAS package. + Cflags: -I${openblasCompat}/include + Libs: -L${openblasCompat}/lib -lopenblas + ''; +} diff --git a/pkgs/applications/science/math/sage/patchSageShebangs.sh b/pkgs/applications/science/math/sage/patchSageShebangs.sh deleted file mode 100644 index 6ddf93af0114..000000000000 --- a/pkgs/applications/science/math/sage/patchSageShebangs.sh +++ /dev/null @@ -1,51 +0,0 @@ -# This is a slightly modified version of nix's default patchShebangs - -dir="$1" - -echo "patching sage internal script interpreter paths in $( readlink -f "$dir")" - -find "$dir" -type f -perm -0100 | while read f; do - if [ "$(head -1 "$f" | head -c+2)" != '#!' ]; then - # missing shebang => not a script - continue - fi - - oldInterpreterLine=$(head -1 "$f" | tail -c+3) - read -r oldPath arg0 args <<< "$oldInterpreterLine" - - if $(echo "$oldPath" | grep -q "/bin/env$"); then - # Check for unsupported 'env' functionality: - # - options: something starting with a '-' - # - environment variables: foo=bar - if $(echo "$arg0" | grep -q -- "^-.*\|.*=.*"); then - echo "unsupported interpreter directive \"$oldInterpreterLine\" (set dontPatchShebangs=1 and handle shebang patching yourself)" - exit 1 - fi - executable="$arg0" - else - if [ "$oldPath" = "" ]; then - # If no interpreter is specified linux will use /bin/sh. Set - # oldpath="/bin/sh" so that we get /nix/store/.../sh. - oldPath="/bin/sh" - fi - executable="$(basename "$oldPath")" - args="$arg0 $args" - fi - - newPath="$(echo "$out/bin/$executable $args" | sed 's/[[:space:]]*$//')" - if [[ ! -x "$newPath" ]] ; then - newPath="$(command -v "$executable" || true)" - fi - - # Strip trailing whitespace introduced when no arguments are present - newInterpreterLine="$(echo "$newPath $args" | sed 's/[[:space:]]*$//')" - - if [ -n "$oldPath" -a "${oldPath:0:${#NIX_STORE}}" != "$NIX_STORE" ]; then - if [ -n "$newPath" -a "$newPath" != "$oldPath" ]; then - echo "$f: sage interpreter directive changed from \"$oldInterpreterLine\" to \"$newInterpreterLine\"" - # escape the escape chars so that sed doesn't interpret them - escapedInterpreterLine=$(echo "$newInterpreterLine" | sed 's|\\|\\\\|g') - sed -i -e "1 s|.*|#\!$escapedInterpreterLine|" "$f" - fi - fi -done diff --git a/pkgs/applications/science/math/sage/patches/arb-2.13.0.patch b/pkgs/applications/science/math/sage/patches/arb-2.13.0.patch new file mode 100644 index 000000000000..a20f1670a256 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/arb-2.13.0.patch @@ -0,0 +1,427 @@ +commit c885927e25b29bd23869e02379c2918da430323e +Author: Timo Kaufmann +Date: Sat Jun 30 02:26:15 2018 +0200 + +diff --git a/build/pkgs/arb/checksums.ini b/build/pkgs/arb/checksums.ini +index 1924ee03c3..9323b97391 100644 +--- a/build/pkgs/arb/checksums.ini ++++ b/build/pkgs/arb/checksums.ini +@@ -1,4 +1,4 @@ + tarball=arb-VERSION.tar.gz +-sha1=27476d0529e48a07d92da90bd0fb80dd18f443e3 +-md5=733285d9705d10b8024e551ffa81952f +-cksum=2391183744 ++sha1=44eda7bf8eaa666c45b1fc2c1b5bd08756d94b58 ++md5=fa24de9fffe4394fb6a7a6792e2ecc5f ++cksum=3689220688 +diff --git a/build/pkgs/arb/package-version.txt b/build/pkgs/arb/package-version.txt +index c8810e9bdb..fb2c0766b7 100644 +--- a/build/pkgs/arb/package-version.txt ++++ b/build/pkgs/arb/package-version.txt +@@ -1 +1 @@ +-2.12.0.p0 ++2.13.0 +diff --git a/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch b/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch +deleted file mode 100644 +index 3e5c0e708b..0000000000 +--- a/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch ++++ /dev/null +@@ -1,17 +0,0 @@ +-In newer binutils, ld options -r and -pie conflict. +-Patch due to Jörg-Volker Peetz +-(source : https://groups.google.com/d/msg/sage-devel/TduebNoZuBE/sEULolL0BQAJ), +-packaged by Emmanuel Charpentier +- +-diff -ru arb-2.8.1-orig/Makefile.subdirs arb-2.8.1-new/Makefile.subdirs +---- arb-2.8.1-orig/Makefile.subdirs 2015-12-31 17:30:01.000000000 +0100 +-+++ arb-2.8.1-new/Makefile.subdirs 2016-11-07 18:50:34.540051779 +0100 +-@@ -52,7 +52,7 @@ +- $(QUIET_CC) $(CC) $(CFLAGS) $(INCS) -c $< -o $@ -MMD -MP -MF "$(BUILD_DIR)/$(MOD_DIR)_$*.d" -MT "$(BUILD_DIR)/$(MOD_DIR)_$*.d" -MT "$@" +- +- $(MOD_LOBJ): $(LOBJS) +-- $(QUIET_CC) $(CC) $(ABI_FLAG) -Wl,-r $^ -o $@ -nostdlib +-+ $(QUIET_CC) $(CC) $(ABI_FLAG) -r $^ -o $@ -nostdlib +- +- -include $(LOBJS:.lo=.d) +- +diff --git a/src/sage/rings/complex_arb.pyx b/src/sage/rings/complex_arb.pyx +index 70d51e655a..00e7caea2c 100644 +--- a/src/sage/rings/complex_arb.pyx ++++ b/src/sage/rings/complex_arb.pyx +@@ -857,14 +857,14 @@ class ComplexBallField(UniqueRepresentation, Field): + [0.500000000000000 +/- 2.09e-16] + + sage: CBF.integral(lambda x, _: x.gamma(), 1 - CBF(i), 1 + CBF(i)) +- [+/- 3.95e-15] + [1.5723926694981 +/- 4.53e-14]*I ++ [+/- 4...e-15] + [1.5723926694981 +/- 4...e-14]*I + + sage: C = ComplexBallField(100) + sage: C.integral(lambda x, _: x.cos() * x.sin(), 0, 1) + [0.35403670913678559674939205737 +/- 8.89e-30] + + sage: CBF.integral(lambda x, _: (x + x.exp()).sin(), 0, 8) +- [0.34740017266 +/- 6.36e-12] ++ [0.34740017266 +/- 6...e-12] + + sage: C = ComplexBallField(2000) + sage: C.integral(lambda x, _: (x + x.exp()).sin(), 0, 8) # long time +@@ -879,14 +879,14 @@ class ComplexBallField(UniqueRepresentation, Field): + ....: else: + ....: return z.sqrt() + sage: CBF.integral(my_sqrt, -1 + CBF(i), -1 - CBF(i)) +- [+/- 1.14e-14] + [-0.4752076627926 +/- 5.18e-14]*I ++ [+/- 1.14e-14] + [-0.4752076627926 +/- 5...e-14]*I + + Note, though, that proper handling of the ``analytic`` flag is required + even when the path does not touch the branch cut:: + + sage: correct = CBF.integral(my_sqrt, 1, 2); correct + [1.21895141649746 +/- 3.73e-15] +- sage: RBF(integral(sqrt(x), x, 1, 2)) ++ sage: RBF(integral(sqrt(x), x, 1, 2)) # long time + [1.21895141649746 +/- 1.79e-15] + sage: wrong = CBF.integral(lambda z, _: z.sqrt(), 1, 2) # WRONG! + sage: correct - wrong +@@ -915,9 +915,9 @@ class ComplexBallField(UniqueRepresentation, Field): + the integrand is unbounded:: + + sage: CBF.integral(lambda x, _: 1/x, -1, 1) +- [+/- inf] + [+/- inf]*I ++ nan + nan*I + sage: CBF.integral(lambda x, _: 1/x, 10^-1000, 1) +- [+/- inf] + [+/- inf]*I ++ nan + nan*I + sage: CBF.integral(lambda x, _: 1/x, 10^-1000, 1, abs_tol=1e-10) + [2302.5850930 +/- 1.26e-8] + +@@ -928,14 +928,15 @@ class ComplexBallField(UniqueRepresentation, Field): + sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, abs_tol=1e-450) + [2.304377150950e-439 +/- 9.74e-452] + sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, abs_tol=0) +- [2.304377150949e-439 +/- 7.53e-452] +- sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, rel_tol=1e-4, abs_tol=0) +- [2.30438e-439 +/- 3.90e-445] ++ [2.304377150950e-439 +/- 7...e-452] ++ sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, rel_tol=1e-2, abs_tol=0) ++ [2.30438e-439 +/- 5.94e-445] + +- sage: CBF.integral(lambda x, _: x*(1/x).sin(), 0, 1) +- [+/- 0.644] +- sage: CBF.integral(lambda x, _: x*(1/x).sin(), 0, 1, use_heap=True) +- [0.3785300 +/- 4.32e-8] ++ sage: epsi = CBF(1e-10) ++ sage: CBF.integral(lambda x, _: x*(1/x).sin(), epsi, 1) ++ [0.38 +/- 8.54e-3] ++ sage: CBF.integral(lambda x, _: x*(1/x).sin(), epsi, 1, use_heap=True) ++ [0.37853002 +/- 8.73e-9] + + ALGORITHM: + +@@ -951,12 +952,12 @@ class ComplexBallField(UniqueRepresentation, Field): + + sage: i = QuadraticField(-1).gen() + sage: CBF.integral(lambda x, _: (1 + i*x).gamma(), -1, 1) +- [1.5723926694981 +/- 4.53e-14] + [+/- 3.95e-15]*I ++ [1.5723926694981 +/- 4...e-14] + [+/- 4...e-15]*I + +- sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, rel_tol=1e-400) +- [0.459... +/- ...e-4...] ++ sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, rel_tol=1e-300) ++ [0.459... +/- ...e-3...] + sage: CBF.integral(lambda x, _: x.sin(), 0, 100, rel_tol=10) +- [+/- 7.61] ++ [0.138 +/- 5.53e-4] + + sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, abs_tol=1e-400) + [0.459697... +/- ...e-4...] +@@ -2389,9 +2390,9 @@ cdef class ComplexBall(RingElement): + sage: ~CBF(i/3) + [-3.00000000000000 +/- 9.44e-16]*I + sage: ~CBF(0) +- [+/- inf] ++ nan + sage: ~CBF(RIF(10,11)) +- [0.1 +/- 9.53e-3] ++ [0.1 +/- 9.10e-3] + """ + cdef ComplexBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -2512,9 +2513,9 @@ cdef class ComplexBall(RingElement): + sage: CBF(-2, 1)/CBF(1, 1/3) + [-1.500000000000000 +/- 8.83e-16] + [1.500000000000000 +/- 5.64e-16]*I + sage: CBF(2+I)/CBF(0) +- [+/- inf] + [+/- inf]*I ++ nan + nan*I + sage: CBF(1)/CBF(0) +- [+/- inf] ++ nan + sage: CBF(1)/CBF(RBF(0, 1.)) + nan + """ +@@ -2543,9 +2544,9 @@ cdef class ComplexBall(RingElement): + sage: CBF(0)^(1/3) + 0 + sage: CBF(0)^(-1) +- [+/- inf] ++ nan + sage: CBF(0)^(-2) +- [+/- inf] + [+/- inf]*I ++ nan + nan*I + + TESTS:: + +@@ -2656,12 +2657,12 @@ cdef class ComplexBall(RingElement): + sage: CBF(1).rising_factorial(5) + 120.0000000000000 + sage: CBF(1/3, 1/2).rising_factorial(300) +- [-3.87949484514e+612 +/- 5.23e+600] + [-3.52042209763e+612 +/- 5.55e+600]*I ++ [-3.87949484514e+612 +/- 5...e+600] + [-3.52042209763e+612 +/- 5...e+600]*I + + sage: CBF(1).rising_factorial(-1) + nan + sage: CBF(1).rising_factorial(2**64) +- [+/- 2.30e+347382171305201370464] ++ [+/- 2.30e+347382171326740403407] + sage: ComplexBallField(128)(1).rising_factorial(2**64) + [2.343691126796861348e+347382171305201285713 +/- 4.71e+347382171305201285694] + sage: CBF(1/2).rising_factorial(CBF(2,3)) +@@ -2700,7 +2701,7 @@ cdef class ComplexBall(RingElement): + [1.000000000000000 +/- 2.83e-16] + [-0.441271200305303 +/- 2.82e-16]*I + + sage: CBF('inf').log() +- nan + nan*I ++ [+/- inf] + sage: CBF(2).log(0) + nan + nan*I + """ +@@ -2808,7 +2809,7 @@ cdef class ComplexBall(RingElement): + sage: CBF(pi/2, 1/10).tan() + [+/- 2.87e-14] + [10.0333111322540 +/- 2.36e-14]*I + sage: CBF(pi/2).tan() +- [+/- inf] ++ nan + """ + cdef ComplexBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -2825,7 +2826,7 @@ cdef class ComplexBall(RingElement): + sage: CBF(pi, 1/10).cot() + [+/- 5.74e-14] + [-10.0333111322540 +/- 2.81e-14]*I + sage: CBF(pi).cot() +- [+/- inf] ++ nan + """ + cdef ComplexBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -3211,9 +3212,9 @@ cdef class ComplexBall(RingElement): + 1.000000000000000*I + + sage: CBF(2+3*I).hypergeometric([1/4,1/3],[1/2]) +- [0.7871684267473 +/- 7.34e-14] + [0.2749254173721 +/- 9.23e-14]*I ++ [0.7871684267473 +/- 7...e-14] + [0.2749254173721 +/- 9...e-14]*I + sage: CBF(2+3*I).hypergeometric([1/4,1/3],[1/2],regularized=True) +- [0.4441122268685 +/- 3.96e-14] + [0.1551100567338 +/- 5.75e-14]*I ++ [0.4441122268685 +/- 3...e-14] + [0.1551100567338 +/- 5...e-14]*I + + sage: CBF(5).hypergeometric([2,3], [-5]) + nan + nan*I +@@ -4041,9 +4042,9 @@ cdef class ComplexBall(RingElement): + + sage: phi = CBF(1,1) + sage: (CBF.pi()/2).elliptic_e_inc(phi) +- [1.283840957898 +/- 3.23e-13] + [-0.5317843366915 +/- 7.79e-14]*I ++ [1.283840957898 +/- 3...e-13] + [-0.5317843366915 +/- 7...e-14]*I + sage: phi.elliptic_e() +- [1.2838409578982 +/- 5.90e-14] + [-0.5317843366915 +/- 3.35e-14]*I ++ [1.2838409578982 +/- 5...e-14] + [-0.5317843366915 +/- 3...e-14]*I + + sage: phi = CBF(2, 3/7) + sage: (CBF.pi()/2).elliptic_e_inc(phi) +@@ -4312,8 +4313,7 @@ cdef class ComplexBall(RingElement): + sage: CBF(10).laguerre_L(3, 2) + [-6.666666666667 +/- 4.15e-13] + sage: CBF(5,7).laguerre_L(CBF(2,3), CBF(1,-2)) +- [5515.315030271 +/- 4.37e-10] + [-12386.942845271 +/- 5.47e-10]*I +- ++ [5515.315030271 +/- 4...e-10] + [-12386.942845271 +/- 5...e-10]*I + """ + cdef ComplexBall my_n = self._parent.coerce(n) + cdef ComplexBall my_m = self._parent.coerce(m) +@@ -4357,9 +4357,9 @@ cdef class ComplexBall(RingElement): + EXAMPLES:: + + sage: CBF(1/2).legendre_P(5) +- [0.08984375000000000 +/- 4.5...e-18] ++ [0.0898437500000000 +/- 7...e-17] + sage: CBF(1,2).legendre_P(CBF(2,3), CBF(0,1)) +- [0.10996180744364 +/- 7.45e-15] + [0.14312767804055 +/- 8.38e-15]*I ++ [0.10996180744364 +/- 7.12e-15] + [0.14312767804055 +/- 8.07e-15]*I + sage: CBF(-10).legendre_P(5, 325/100) + [-22104403.487377 +/- 6.81e-7] + [53364750.687392 +/- 7.25e-7]*I + sage: CBF(-10).legendre_P(5, 325/100, type=3) +@@ -4393,9 +4393,9 @@ cdef class ComplexBall(RingElement): + sage: CBF(1/2).legendre_Q(5) + [0.55508089057168 +/- 2.79e-15] + sage: CBF(1,2).legendre_Q(CBF(2,3), CBF(0,1)) +- [0.167678710 +/- 4.60e-10] + [-0.161558598 +/- 7.47e-10]*I ++ [0.167678710 +/- 3.91e-10] + [-0.161558598 +/- 6.77e-10]*I + sage: CBF(-10).legendre_Q(5, 325/100) +- [-83825154.36008 +/- 4.94e-6] + [-34721515.80396 +/- 5.40e-6]*I ++ [-83825154.36008 +/- 5.02e-6] + [-34721515.80396 +/- 5.42e-6]*I + sage: CBF(-10).legendre_Q(5, 325/100, type=3) + [-4.797306921692e-6 +/- 6.82e-19] + [-4.797306921692e-6 +/- 6.57e-19]*I + +diff --git a/src/sage/rings/polynomial/polynomial_complex_arb.pyx b/src/sage/rings/polynomial/polynomial_complex_arb.pyx +index c436d4705b..ef611a566b 100644 +--- a/src/sage/rings/polynomial/polynomial_complex_arb.pyx ++++ b/src/sage/rings/polynomial/polynomial_complex_arb.pyx +@@ -543,7 +543,7 @@ cdef class Polynomial_complex_arb(Polynomial): + sage: (1 - x/3).inverse_series_trunc(3) + ([0.1111111111111111 +/- 5.99e-17])*x^2 + ([0.3333333333333333 +/- 7.04e-17])*x + 1.000000000000000 + sage: x.inverse_series_trunc(1) +- [+/- inf] ++ nan + sage: Pol(0).inverse_series_trunc(2) + (nan + nan*I)*x + nan + nan*I + +@@ -671,7 +671,7 @@ cdef class Polynomial_complex_arb(Polynomial): + sage: pol._sqrt_series(2) + ([+/- 7.51e-3] + [+/- 0.501]*I)*x + [+/- 5.01e-3] + [+/- 1.01]*I + sage: x._sqrt_series(2) +- ([+/- inf] + [+/- inf]*I)*x ++ (nan + nan*I)*x + """ + cdef Polynomial_complex_arb res = self._new() + if n < 0: +diff --git a/src/sage/rings/real_arb.pyx b/src/sage/rings/real_arb.pyx +index c9f68e38d7..76e3037a9a 100644 +--- a/src/sage/rings/real_arb.pyx ++++ b/src/sage/rings/real_arb.pyx +@@ -161,7 +161,7 @@ values and should be preferred:: + + sage: RBF(NaN) < RBF(infinity) + False +- sage: 1/RBF(0) <= RBF(infinity) ++ sage: RBF(0).add_error(infinity) <= RBF(infinity) + True + + TESTS:: +@@ -252,6 +252,8 @@ cdef void mpfi_to_arb(arb_t target, const mpfi_t source, const long precision): + (+infinity, +infinity) + sage: RBF(RIF(-infinity)).endpoints() + (-infinity, -infinity) ++ sage: RBF(RIF(-infinity, infinity)).endpoints() ++ (-infinity, +infinity) + sage: RIF(RBF(infinity)).endpoints() + (+infinity, +infinity) + sage: RIF(RBF(-infinity)).endpoints() +@@ -266,10 +268,11 @@ cdef void mpfi_to_arb(arb_t target, const mpfi_t source, const long precision): + if _do_sig(precision): sig_on() + mpfi_get_left(left, source) + mpfi_get_right(right, source) +- arb_set_interval_mpfr(target, left, right, precision) +- # Work around weakness of arb_set_interval_mpfr(tgt, inf, inf) +- if mpfr_equal_p(left, right): +- mag_zero(arb_radref(target)) ++ if mpfr_inf_p(left) and mpfr_inf_p(right) and mpfr_sgn(left) < 0 < mpfr_sgn(right): ++ # Work around a weakness of arb_set_interval_mpfr(tgt, -inf, inf) ++ arb_zero_pm_inf(target) ++ else: ++ arb_set_interval_mpfr(target, left, right, precision) + if _do_sig(precision): sig_off() + + mpfr_clear(left) +@@ -649,17 +652,15 @@ class RealBallField(UniqueRepresentation, Field): + EXAMPLES:: + + sage: RBF.some_elements() +- [1.000000000000000, +- [0.3333333333333333 +/- 7.04e-17], ++ [0, 1.000000000000000, [0.3333333333333333 +/- 7.04e-17], + [-4.733045976388941e+363922934236666733021124 +/- 3.46e+363922934236666733021108], +- [+/- inf], +- [+/- inf], +- nan] ++ [+/- inf], [+/- inf], [+/- inf], nan] + """ + import sage.symbolic.constants +- return [self(1), self(1)/3, ++ inf = self(sage.rings.infinity.Infinity) ++ return [self(0), self(1), self(1)/3, + -self(2)**(Integer(2)**80), +- self(sage.rings.infinity.Infinity), ~self(0), ++ inf, -inf, self.zero().add_error(inf), + self.element_class(self, sage.symbolic.constants.NotANumber())] + + def _sum_of_products(self, terms): +@@ -881,7 +882,7 @@ class RealBallField(UniqueRepresentation, Field): + sage: RBF.gamma(5) + 24.00000000000000 + sage: RBF.gamma(10**20) +- [+/- 5.92e+1956570551809674821757] ++ [+/- 5.50e+1956570552410610660600] + sage: RBF.gamma(1/3) + [2.678938534707747 +/- 8.99e-16] + sage: RBF.gamma(-5) +@@ -2247,7 +2248,7 @@ cdef class RealBall(RingElement): + sage: inf = RBF(+infinity) + sage: other_inf = RBF(+infinity, 42.r) + sage: neg_inf = RBF(-infinity) +- sage: extended_line = 1/RBF(0) ++ sage: extended_line = RBF(0).add_error(infinity) + sage: exact_nan = inf - inf + sage: exact_nan.mid(), exact_nan.rad() + (NaN, 0.00000000) +@@ -2659,7 +2660,7 @@ cdef class RealBall(RingElement): + sage: ~RBF(5) + [0.2000000000000000 +/- 4.45e-17] + sage: ~RBF(0) +- [+/- inf] ++ nan + sage: RBF(RIF(-0.1,0.1)) + [+/- 0.101] + +@@ -2739,7 +2740,7 @@ cdef class RealBall(RingElement): + sage: RBF(pi)/RBF(e) + [1.155727349790922 +/- 8.43e-16] + sage: RBF(2)/RBF(0) +- [+/- inf] ++ nan + """ + cdef RealBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -2765,7 +2766,7 @@ cdef class RealBall(RingElement): + sage: RBF(-1)^(1/3) + nan + sage: RBF(0)^(-1) +- [+/- inf] ++ nan + sage: RBF(-e)**RBF(pi) + nan + +@@ -3129,7 +3130,7 @@ cdef class RealBall(RingElement): + sage: RBF(1).tan() + [1.557407724654902 +/- 3.26e-16] + sage: RBF(pi/2).tan() +- [+/- inf] ++ nan + """ + cdef RealBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -3146,7 +3147,7 @@ cdef class RealBall(RingElement): + sage: RBF(1).cot() + [0.642092615934331 +/- 4.79e-16] + sage: RBF(pi).cot() +- [+/- inf] ++ nan + """ + cdef RealBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -3257,7 +3258,7 @@ cdef class RealBall(RingElement): + sage: RBF(1).coth() + [1.313035285499331 +/- 4.97e-16] + sage: RBF(0).coth() +- [+/- inf] ++ nan + """ + cdef RealBall res = self._new() + if _do_sig(prec(self)): sig_on() diff --git a/pkgs/applications/science/math/sage/patches/dochtml-optional.patch b/pkgs/applications/science/math/sage/patches/dochtml-optional.patch new file mode 100644 index 000000000000..a51e30312ed9 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/dochtml-optional.patch @@ -0,0 +1,127 @@ +diff --git a/src/doc/common/conf.py b/src/doc/common/conf.py +index 25f94f7b7d..9f6139ea4a 100644 +--- a/src/doc/common/conf.py ++++ b/src/doc/common/conf.py +@@ -622,9 +622,9 @@ def call_intersphinx(app, env, node, contnode): + Check that the link from the thematic tutorials to the reference + manual is relative, see :trac:`20118`:: + +- sage: from sage.env import SAGE_DOC +- sage: thematic_index = os.path.join(SAGE_DOC, "html", "en", "thematic_tutorials", "index.html") +- sage: for line in open(thematic_index).readlines(): ++ sage: from sage.env import SAGE_DOC # optional - dochtml ++ sage: thematic_index = os.path.join(SAGE_DOC, "html", "en", "thematic_tutorials", "index.html") # optional - dochtml ++ sage: for line in open(thematic_index).readlines(): # optional - dochtml + ....: if "padics" in line: + ....: sys.stdout.write(line) +
  • Introduction to the -adics
    • +diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py +index 4236fd05e0..8e499cbaf7 100644 +--- a/src/sage/doctest/control.py ++++ b/src/sage/doctest/control.py +@@ -87,7 +87,7 @@ class DocTestDefaults(SageObject): + self.sagenb = False + self.long = False + self.warn_long = None +- self.optional = set(['sage']) | auto_optional_tags ++ self.optional = set(['sage', 'dochtml']) | auto_optional_tags + self.randorder = None + self.global_iterations = 1 # sage-runtests default is 0 + self.file_iterations = 1 # sage-runtests default is 0 +@@ -343,7 +343,8 @@ class DocTestController(SageObject): + if not optionaltag_regex.search(o): + raise ValueError('invalid optional tag {!r}'.format(o)) + +- options.optional |= auto_optional_tags ++ if "sage" in options.optional: ++ options.optional |= auto_optional_tags + + self.options = options + self.files = args +@@ -741,7 +742,7 @@ class DocTestController(SageObject): + sage: DC = DocTestController(DD, [dirname]) + sage: DC.expand_files_into_sources() + sage: sorted(DC.sources[0].options.optional) # abs tol 1 +- ['guava', 'magma', 'py3'] ++ ['guava', 'magma'] + + We check that files are skipped appropriately:: + +@@ -968,7 +969,7 @@ class DocTestController(SageObject): + sage: from sage.doctest.control import DocTestDefaults, DocTestController + sage: DC = DocTestController(DocTestDefaults(), []) + sage: DC._optional_tags_string() +- 'sage' ++ 'dochtml,sage' + sage: DC = DocTestController(DocTestDefaults(optional="all,and,some,more"), []) + sage: DC._optional_tags_string() + 'all' +diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py +index 9255aa848f..cc4712d3ec 100644 +--- a/src/sage/misc/sagedoc.py ++++ b/src/sage/misc/sagedoc.py +@@ -18,9 +18,9 @@ TESTS: + Check that argspecs of extension function/methods appear correctly, + see :trac:`12849`:: + +- sage: from sage.env import SAGE_DOC +- sage: docfilename = os.path.join(SAGE_DOC, 'html', 'en', 'reference', 'calculus', 'sage', 'symbolic', 'expression.html') +- sage: with open(docfilename) as fobj: ++ sage: from sage.env import SAGE_DOC # optional - dochtml ++ sage: docfilename = os.path.join(SAGE_DOC, 'html', 'en', 'reference', 'calculus', 'sage', 'symbolic', 'expression.html') # optional - dochtml ++ sage: with open(docfilename) as fobj: # optional - dochtml + ....: for line in fobj: + ....: if "#sage.symbolic.expression.Expression.numerical_approx" in line: + ....: print(line) +@@ -790,11 +790,12 @@ def _search_src_or_doc(what, string, extra1='', extra2='', extra3='', + + :: + +- sage: len(_search_src_or_doc('src', r'matrix\(', 'incidence_structures', 'self', 'combinat', interact=False).splitlines()) > 1 ++ sage: from sage.misc.sagedoc import _search_src_or_doc # optional - dochtml ++ sage: len(_search_src_or_doc('src', r'matrix\(', 'incidence_structures', 'self', 'combinat', interact=False).splitlines()) > 1 # optional - dochtml + True +- sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology', 'variety', interact=False) # long time (4s on sage.math, 2012) ++ sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology', 'variety', interact=False) # optional - dochtml, long time (4s on sage.math, 2012) + True +- sage: 'divisors' in _search_src_or_doc('src', '^ *def prime', interact=False) ++ sage: 'divisors' in _search_src_or_doc('src', '^ *def prime', interact=False) # optional - dochtml + True + """ + # process keywords +@@ -1160,9 +1161,9 @@ def search_doc(string, extra1='', extra2='', extra3='', extra4='', + counting the length of ``search_doc('tree', + interact=False).splitlines()`` gives the number of matches. :: + +- sage: len(search_doc('tree', interact=False).splitlines()) > 4000 # long time ++ sage: len(search_doc('tree', interact=False).splitlines()) > 4000 # optional - dochtml, long time + True +- sage: len(search_doc('tree', whole_word=True, interact=False).splitlines()) < 2000 # long time ++ sage: len(search_doc('tree', whole_word=True, interact=False).splitlines()) < 2000 # optional - dochtml, long time + True + """ + return _search_src_or_doc('doc', string, extra1=extra1, extra2=extra2, +@@ -1332,9 +1333,9 @@ class _sage_doc: + + EXAMPLES:: + +- sage: browse_sage_doc._open("reference", testing=True)[0] # indirect doctest ++ sage: browse_sage_doc._open("reference", testing=True)[0] # optional - dochtml, indirect doctest + 'http://localhost:8000/doc/live/reference/index.html' +- sage: browse_sage_doc(identity_matrix, 'rst')[-107:-47] ++ sage: browse_sage_doc(identity_matrix, 'rst')[-107:-47] # optional - dochtml + 'Full MatrixSpace of 3 by 3 sparse matrices over Integer Ring' + """ + def __init__(self): +@@ -1494,9 +1495,9 @@ class _sage_doc: + + EXAMPLES:: + +- sage: browse_sage_doc._open("reference", testing=True)[0] ++ sage: browse_sage_doc._open("reference", testing=True)[0] # optional - dochtml + 'http://localhost:8000/doc/live/reference/index.html' +- sage: browse_sage_doc._open("tutorial", testing=True)[1] ++ sage: browse_sage_doc._open("tutorial", testing=True)[1] # optional - dochtml + '.../html/en/tutorial/index.html' + """ + url = self._base_url + os.path.join(name, "index.html") diff --git a/pkgs/applications/science/math/sage/patches/eclib-regulator-precision.patch b/pkgs/applications/science/math/sage/patches/eclib-regulator-precision.patch new file mode 100644 index 000000000000..a1464b8fe310 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/eclib-regulator-precision.patch @@ -0,0 +1,98 @@ +diff --git a/src/sage/libs/eclib/interface.py b/src/sage/libs/eclib/interface.py +index f77000c478..9d17d412ae 100644 +--- a/src/sage/libs/eclib/interface.py ++++ b/src/sage/libs/eclib/interface.py +@@ -1014,7 +1014,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 2 will not be done; + ... + Gained index 2 +- New regulator = 93.857300720636393209 ++ New regulator = 93.85730... + (False, 2, '[ ]') + sage: EQ.points() + [[-2, 3, 1], [2707496766203306, 864581029138191, 2969715140223272], [-13422227300, -49322830557, 12167000000]] +@@ -1025,7 +1025,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 3 will not be done; + ... + Gained index 3 +- New regulator = 10.4285889689595992455 ++ New regulator = 10.42858... + (False, 3, '[ ]') + sage: EQ.points() + [[-2, 3, 1], [-14, 25, 8], [-13422227300, -49322830557, 12167000000]] +@@ -1036,7 +1036,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 5 will not be done; + ... + Gained index 5 +- New regulator = 0.417143558758383969818 ++ New regulator = 0.41714... + (False, 5, '[ ]') + sage: EQ.points() + [[-2, 3, 1], [-14, 25, 8], [1, -1, 1]] +@@ -1221,7 +1221,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 2 will not be done; + ... + Gained index 2 +- New regulator = 93.857300720636393209 ++ New regulator = 93.85730... + (False, 2, '[ ]') + sage: EQ + Subgroup of Mordell-Weil group: [[-2:3:1], [2707496766203306:864581029138191:2969715140223272], [-13422227300:-49322830557:12167000000]] +@@ -1235,7 +1235,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 3 will not be done; + ... + Gained index 3 +- New regulator = 10.4285889689595992455 ++ New regulator = 10.42858... + (False, 3, '[ ]') + sage: EQ + Subgroup of Mordell-Weil group: [[-2:3:1], [-14:25:8], [-13422227300:-49322830557:12167000000]] +@@ -1249,7 +1249,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 5 will not be done; + ... + Gained index 5 +- New regulator = 0.417143558758383969818 ++ New regulator = 0.41714... + (False, 5, '[ ]') + sage: EQ + Subgroup of Mordell-Weil group: [[-2:3:1], [-14:25:8], [1:-1:1]] +diff --git a/src/sage/libs/eclib/mwrank.pyx b/src/sage/libs/eclib/mwrank.pyx +index a4f89e1ca5..f8a22d2f55 100644 +--- a/src/sage/libs/eclib/mwrank.pyx ++++ b/src/sage/libs/eclib/mwrank.pyx +@@ -1234,9 +1234,9 @@ cdef class _two_descent: + sage: D2.saturate() + Searching for points (bound = 8)...done: + found points which generate a subgroup of rank 3 +- and regulator 0.417143558758383969817119544618093396749810106098479 ++ and regulator 0.41714... + Processing points found during 2-descent...done: +- now regulator = 0.417143558758383969817119544618093396749810106098479 ++ now regulator = 0.41714... + No saturation being done + sage: D2.getbasis() + '[[1:-1:1], [-2:3:1], [-14:25:8]]' +@@ -1281,9 +1281,9 @@ cdef class _two_descent: + sage: D2.saturate() + Searching for points (bound = 8)...done: + found points which generate a subgroup of rank 3 +- and regulator 0.417143558758383969817119544618093396749810106098479 ++ and regulator 0.41714... + Processing points found during 2-descent...done: +- now regulator = 0.417143558758383969817119544618093396749810106098479 ++ now regulator = 0.41714... + No saturation being done + sage: D2.getbasis() + '[[1:-1:1], [-2:3:1], [-14:25:8]]' +@@ -1329,9 +1329,9 @@ cdef class _two_descent: + sage: D2.saturate() + Searching for points (bound = 8)...done: + found points which generate a subgroup of rank 3 +- and regulator 0.417143558758383969817119544618093396749810106098479 ++ and regulator 0.41714... + Processing points found during 2-descent...done: +- now regulator = 0.417143558758383969817119544618093396749810106098479 ++ now regulator = 0.41714... + No saturation being done + sage: D2.getbasis() + '[[1:-1:1], [-2:3:1], [-14:25:8]]' diff --git a/pkgs/applications/science/math/sage/patches/matplotlib-normed-deprecated.patch b/pkgs/applications/science/math/sage/patches/matplotlib-normed-deprecated.patch new file mode 100644 index 000000000000..41747635cacd --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/matplotlib-normed-deprecated.patch @@ -0,0 +1,12 @@ +diff --git a/src/sage/all.py b/src/sage/all.py +index 14cec431f1..25a35a0522 100644 +--- a/src/sage/all.py ++++ b/src/sage/all.py +@@ -310,6 +310,7 @@ warnings.filters.remove(('ignore', None, DeprecationWarning, None, 0)) + # Ignore all deprecations from IPython etc. + warnings.filterwarnings('ignore', + module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic)') ++warnings.filterwarnings('ignore', "The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.") # matplotlib normed deprecation + # However, be sure to keep OUR deprecation warnings + warnings.filterwarnings('default', + '[\s\S]*See http://trac.sagemath.org/[0-9]* for details.') diff --git a/pkgs/applications/science/math/sage/patches/maxima-5.41.0-doctests.patch b/pkgs/applications/science/math/sage/patches/maxima-5.41.0-doctests.patch new file mode 100644 index 000000000000..fad434e52ada --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/maxima-5.41.0-doctests.patch @@ -0,0 +1,48 @@ +diff --git a/src/sage/interfaces/maxima_abstract.py b/src/sage/interfaces/maxima_abstract.py +index 961c20aaac..3d601d8939 100644 +--- a/src/sage/interfaces/maxima_abstract.py ++++ b/src/sage/interfaces/maxima_abstract.py +@@ -1743,7 +1743,7 @@ class MaximaAbstractElement(ExtraTabCompletion, InterfaceElement): + sage: y,d = var('y,d') + sage: f = function('f') + sage: latex(maxima(derivative(f(x*y), x))) +- \left(\left.{{{\it \partial}}\over{{\it \partial}\, {\it t_0}}}\,f\left({\it t_0}\right) \right|_{{\it t_0}={\it x}\, {\it y}}\right)\,{\it y} ++ \left(\left.{{{\it \partial}}\over{{\it \partial}\, {\it t}_{0}}}\,f\left({\it t}_{0}\right) \right|_{{\it t}_{0}={\it x}\, {\it y}}\right)\,{\it y} + sage: latex(maxima(derivative(f(x,y,d), d,x,x,y))) + {{{\it \partial}^4}\over{{\it \partial}\,{\it d}\, {\it \partial}\,{\it x}^2\,{\it \partial}\, {\it y}}}\,f\left({\it x} , {\it y} , {\it d}\right) + sage: latex(maxima(d/(d-2))) +diff --git a/src/sage/manifolds/differentiable/metric.py b/src/sage/manifolds/differentiable/metric.py +index 3cd6ad3235..1e18af1a6b 100644 +--- a/src/sage/manifolds/differentiable/metric.py ++++ b/src/sage/manifolds/differentiable/metric.py +@@ -993,7 +993,7 @@ class PseudoRiemannianMetric(TensorField): + 2-dimensional differentiable manifold S^2 + sage: g.riemann()[:] + [[[[0, 0], [0, 0]], [[0, sin(th)^2], [-sin(th)^2, 0]]], +- [[[0, (cos(th)^2 - 1)/sin(th)^2], [1, 0]], [[0, 0], [0, 0]]]] ++ [[[0, -1], [1, 0]], [[0, 0], [0, 0]]]] + + In dimension 2, the Riemann tensor can be expressed entirely in terms of + the Ricci scalar `r`: +diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx +index dfb8751467..27402e54ab 100644 +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -7154,7 +7154,7 @@ cdef class Expression(CommutativeRingElement): + sage: ex = lcm(sin(x)^2 - 1, sin(x)^2 + sin(x)); ex + (sin(x)^2 + sin(x))*(sin(x)^2 - 1)/(sin(x) + 1) + sage: ex.simplify_full() +- -cos(x)^2*sin(x) ++ sin(x)^3 - sin(x) + + TESTS: + +@@ -10004,7 +10004,7 @@ cdef class Expression(CommutativeRingElement): + + sage: f=tan(3*x) + sage: f.simplify_trig() +- (4*cos(x)^2 - 1)*sin(x)/(4*cos(x)^3 - 3*cos(x)) ++ -(4*cos(x)^2 - 1)*sin(x)/(4*cos(x)*sin(x)^2 - cos(x)) + sage: f.simplify_trig(False) + sin(3*x)/cos(3*x) + diff --git a/pkgs/applications/science/math/sage/patches/numpy-1.14.3.patch b/pkgs/applications/science/math/sage/patches/numpy-1.14.3.patch new file mode 100644 index 000000000000..5927bc116096 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/numpy-1.14.3.patch @@ -0,0 +1,812 @@ +diff --git a/src/doc/en/faq/faq-usage.rst b/src/doc/en/faq/faq-usage.rst +index 79b4205fd3..9a89bd2136 100644 +--- a/src/doc/en/faq/faq-usage.rst ++++ b/src/doc/en/faq/faq-usage.rst +@@ -338,7 +338,7 @@ ints. For example:: + sage: RealNumber = float; Integer = int + sage: from scipy import stats + sage: stats.ttest_ind(list([1,2,3,4,5]),list([2,3,4,5,.6])) +- Ttest_indResult(statistic=0.076752955645333687, pvalue=0.94070490247380478) ++ Ttest_indResult(statistic=0.0767529..., pvalue=0.940704...) + sage: stats.uniform(0,15).ppf([0.5,0.7]) + array([ 7.5, 10.5]) + +diff --git a/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst b/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst +index 314811c42b..e5f54ec4c2 100644 +--- a/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst ++++ b/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst +@@ -48,11 +48,13 @@ we could do the following. + sage: B = numpy.array([1.0]*5) + sage: B.shape=(5,1) + sage: print(B) +- [[ 1.] +- [ 1.] +- [ 1.] +- [ 1.] +- [ 1.]] ++ [[1.] ++ [1.] ++ [1.] ++ [1.] ++ [1.]] ++ ++ + sage: print(A) + [ 2.00e+00 3.00e+00 0 0 0 ] + [ 3.00e+00 0 4.00e+00 0 6.00e+00] +diff --git a/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst b/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst +index 5b89cd75ee..e50b2ea5d4 100644 +--- a/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst ++++ b/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst +@@ -84,7 +84,7 @@ well as take slices + sage: l[3] + 3.0 + sage: l[3:6] +- array([ 3., 4., 5.]) ++ array([3., 4., 5.]) + + You can do basic arithmetic operations + +@@ -147,11 +147,11 @@ also do matrix vector multiplication, and matrix addition + sage: n = numpy.matrix([[1,2],[3,4]],dtype=float) + sage: v = numpy.array([[1],[2]],dtype=float) + sage: n*v +- matrix([[ 5.], +- [ 11.]]) ++ matrix([[ 5.], ++ [11.]]) + sage: n+n +- matrix([[ 2., 4.], +- [ 6., 8.]]) ++ matrix([[2., 4.], ++ [6., 8.]]) + + If ``n`` was created with :meth:`numpy.array`, then to do matrix vector + multiplication, you would use ``numpy.dot(n,v)``. +@@ -170,11 +170,11 @@ to manipulate + 22., 23., 24.]) + sage: n.shape=(5,5) + sage: n +- array([[ 0., 1., 2., 3., 4.], +- [ 5., 6., 7., 8., 9.], +- [ 10., 11., 12., 13., 14.], +- [ 15., 16., 17., 18., 19.], +- [ 20., 21., 22., 23., 24.]]) ++ array([[ 0., 1., 2., 3., 4.], ++ [ 5., 6., 7., 8., 9.], ++ [10., 11., 12., 13., 14.], ++ [15., 16., 17., 18., 19.], ++ [20., 21., 22., 23., 24.]]) + + This changes the one-dimensional array into a `5\times 5` array. + +@@ -187,8 +187,8 @@ NumPy arrays can be sliced as well + sage: n=numpy.array(range(25),dtype=float) + sage: n.shape=(5,5) + sage: n[2:4,1:3] +- array([[ 11., 12.], +- [ 16., 17.]]) ++ array([[11., 12.], ++ [16., 17.]]) + + It is important to note that the sliced matrices are references to + the original +@@ -224,8 +224,8 @@ Some particularly useful commands are + + sage: x=numpy.arange(0,2,.1,dtype=float) + sage: x +- array([ 0. , 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1. , +- 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9]) ++ array([0. , 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1. , 1.1, 1.2, ++ 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9]) + + You can see that :meth:`numpy.arange` creates an array of floats increasing by 0.1 + from 0 to 2. There is a useful command :meth:`numpy.r_` that is best explained by example +@@ -240,10 +240,11 @@ from 0 to 2. There is a useful command :meth:`numpy.r_` that is best explained b + sage: Integer=int + sage: n=r_[0.0:5.0] + sage: n +- array([ 0., 1., 2., 3., 4.]) ++ array([0., 1., 2., 3., 4.]) + sage: n=r_[0.0:5.0, [0.0]*5] + sage: n +- array([ 0., 1., 2., 3., 4., 0., 0., 0., 0., 0.]) ++ array([0., 1., 2., 3., 4., 0., 0., 0., 0., 0.]) ++ + + :meth:`numpy.r_` provides a shorthand for constructing NumPy arrays efficiently. + Note in the above ``0.0:5.0`` was shorthand for ``0.0, 1.0, 2.0, 3.0, 4.0``. +@@ -255,7 +256,7 @@ intervals. We can do this as follows + :: + + sage: r_[0.0:5.0:11*j] +- array([ 0. , 0.5, 1. , 1.5, 2. , 2.5, 3. , 3.5, 4. , 4.5, 5. ]) ++ array([0. , 0.5, 1. , 1.5, 2. , 2.5, 3. , 3.5, 4. , 4.5, 5. ]) + + The notation ``0.0:5.0:11*j`` expands to a list of 11 equally space + points between 0 and 5 including both endpoints. Note that ``j`` is the +@@ -287,23 +288,23 @@ an equally spaced grid with `\Delta x = \Delta y = .25` for + sage: y=numpy.r_[0.0:1.0:5*j] + sage: xx,yy= meshgrid(x,y) + sage: xx +- array([[ 0. , 0.25, 0.5 , 0.75, 1. ], +- [ 0. , 0.25, 0.5 , 0.75, 1. ], +- [ 0. , 0.25, 0.5 , 0.75, 1. ], +- [ 0. , 0.25, 0.5 , 0.75, 1. ], +- [ 0. , 0.25, 0.5 , 0.75, 1. ]]) ++ array([[0. , 0.25, 0.5 , 0.75, 1. ], ++ [0. , 0.25, 0.5 , 0.75, 1. ], ++ [0. , 0.25, 0.5 , 0.75, 1. ], ++ [0. , 0.25, 0.5 , 0.75, 1. ], ++ [0. , 0.25, 0.5 , 0.75, 1. ]]) + sage: yy +- array([[ 0. , 0. , 0. , 0. , 0. ], +- [ 0.25, 0.25, 0.25, 0.25, 0.25], +- [ 0.5 , 0.5 , 0.5 , 0.5 , 0.5 ], +- [ 0.75, 0.75, 0.75, 0.75, 0.75], +- [ 1. , 1. , 1. , 1. , 1. ]]) ++ array([[0. , 0. , 0. , 0. , 0. ], ++ [0.25, 0.25, 0.25, 0.25, 0.25], ++ [0.5 , 0.5 , 0.5 , 0.5 , 0.5 ], ++ [0.75, 0.75, 0.75, 0.75, 0.75], ++ [1. , 1. , 1. , 1. , 1. ]]) + sage: f(xx,yy) +- array([[ 0. , 0.0625, 0.25 , 0.5625, 1. ], +- [ 0.0625, 0.125 , 0.3125, 0.625 , 1.0625], +- [ 0.25 , 0.3125, 0.5 , 0.8125, 1.25 ], +- [ 0.5625, 0.625 , 0.8125, 1.125 , 1.5625], +- [ 1. , 1.0625, 1.25 , 1.5625, 2. ]]) ++ array([[0. , 0.0625, 0.25 , 0.5625, 1. ], ++ [0.0625, 0.125 , 0.3125, 0.625 , 1.0625], ++ [0.25 , 0.3125, 0.5 , 0.8125, 1.25 ], ++ [0.5625, 0.625 , 0.8125, 1.125 , 1.5625], ++ [1. , 1.0625, 1.25 , 1.5625, 2. ]]) + + You can see that :meth:`numpy.meshgrid` produces a pair of matrices, here denoted + `xx` and `yy`, such that `(xx[i,j],yy[i,j])` has coordinates +@@ -324,7 +325,7 @@ equation `Ax=b` do + sage: b=numpy.array(range(1,6)) + sage: x=linalg.solve(A,b) + sage: numpy.dot(A,x) +- array([ 1., 2., 3., 4., 5.]) ++ array([1., 2., 3., 4., 5.]) + + This creates a random 5x5 matrix ``A``, and solves `Ax=b` where + ``b=[0.0,1.0,2.0,3.0,4.0]``. There are many other routines in the :mod:`numpy.linalg` +diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx +index df85cce43d..34ea164be0 100644 +--- a/src/sage/calculus/riemann.pyx ++++ b/src/sage/calculus/riemann.pyx +@@ -1191,30 +1191,30 @@ cpdef complex_to_spiderweb(np.ndarray[COMPLEX_T, ndim = 2] z_values, + sage: zval = numpy.array([[0, 1, 1000],[.2+.3j,1,-.3j],[0,0,0]],dtype = numpy.complex128) + sage: deriv = numpy.array([[.1]],dtype = numpy.float64) + sage: complex_to_spiderweb(zval, deriv,deriv, 4,4,[0,0,0],1,False,0.001) +- array([[[ 1., 1., 1.], +- [ 1., 1., 1.], +- [ 1., 1., 1.]], ++ array([[[1., 1., 1.], ++ [1., 1., 1.], ++ [1., 1., 1.]], + +- [[ 1., 1., 1.], +- [ 0., 0., 0.], +- [ 1., 1., 1.]], ++ [[1., 1., 1.], ++ [0., 0., 0.], ++ [1., 1., 1.]], + +- [[ 1., 1., 1.], +- [ 1., 1., 1.], +- [ 1., 1., 1.]]]) ++ [[1., 1., 1.], ++ [1., 1., 1.], ++ [1., 1., 1.]]]) + + sage: complex_to_spiderweb(zval, deriv,deriv, 4,4,[0,0,0],1,True,0.001) +- array([[[ 1. , 1. , 1. ], +- [ 1. , 0.05558355, 0.05558355], +- [ 0.17301243, 0. , 0. ]], ++ array([[[1. , 1. , 1. ], ++ [1. , 0.05558355, 0.05558355], ++ [0.17301243, 0. , 0. ]], + +- [[ 1. , 0.96804683, 0.48044583], +- [ 0. , 0. , 0. ], +- [ 0.77351965, 0.5470393 , 1. ]], ++ [[1. , 0.96804683, 0.48044583], ++ [0. , 0. , 0. ], ++ [0.77351965, 0.5470393 , 1. ]], + +- [[ 1. , 1. , 1. ], +- [ 1. , 1. , 1. ], +- [ 1. , 1. , 1. ]]]) ++ [[1. , 1. , 1. ], ++ [1. , 1. , 1. ], ++ [1. , 1. , 1. ]]]) + """ + cdef Py_ssize_t i, j, imax, jmax + cdef FLOAT_T x, y, mag, arg, width, target, precision, dmag, darg +@@ -1279,14 +1279,14 @@ cpdef complex_to_rgb(np.ndarray[COMPLEX_T, ndim = 2] z_values): + sage: from sage.calculus.riemann import complex_to_rgb + sage: import numpy + sage: complex_to_rgb(numpy.array([[0, 1, 1000]], dtype = numpy.complex128)) +- array([[[ 1. , 1. , 1. ], +- [ 1. , 0.05558355, 0.05558355], +- [ 0.17301243, 0. , 0. ]]]) ++ array([[[1. , 1. , 1. ], ++ [1. , 0.05558355, 0.05558355], ++ [0.17301243, 0. , 0. ]]]) + + sage: complex_to_rgb(numpy.array([[0, 1j, 1000j]], dtype = numpy.complex128)) +- array([[[ 1. , 1. , 1. ], +- [ 0.52779177, 1. , 0.05558355], +- [ 0.08650622, 0.17301243, 0. ]]]) ++ array([[[1. , 1. , 1. ], ++ [0.52779177, 1. , 0.05558355], ++ [0.08650622, 0.17301243, 0. ]]]) + + + TESTS:: +diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py +index 61b1003002..4baee9cbbd 100644 +--- a/src/sage/combinat/fully_packed_loop.py ++++ b/src/sage/combinat/fully_packed_loop.py +@@ -72,11 +72,11 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False): + sage: _make_color_list(5, ['blue', 'red']) + ['blue', 'red', 'blue', 'red', 'blue'] + sage: _make_color_list(5, color_map='summer') +- [(0.0, 0.5, 0.40000000000000002), +- (0.25098039215686274, 0.62549019607843137, 0.40000000000000002), +- (0.50196078431372548, 0.75098039215686274, 0.40000000000000002), +- (0.75294117647058822, 0.87647058823529411, 0.40000000000000002), +- (1.0, 1.0, 0.40000000000000002)] ++ [(0.0, 0.5, 0.4), ++ (0.25098039215686274, 0.6254901960784314, 0.4), ++ (0.5019607843137255, 0.7509803921568627, 0.4), ++ (0.7529411764705882, 0.8764705882352941, 0.4), ++ (1.0, 1.0, 0.4)] + sage: _make_color_list(8, ['blue', 'red'], randomize=True) + ['blue', 'blue', 'red', 'blue', 'red', 'red', 'red', 'blue'] + """ +diff --git a/src/sage/finance/time_series.pyx b/src/sage/finance/time_series.pyx +index c37700d14e..49b7298d0b 100644 +--- a/src/sage/finance/time_series.pyx ++++ b/src/sage/finance/time_series.pyx +@@ -109,8 +109,8 @@ cdef class TimeSeries: + + sage: import numpy + sage: v = numpy.array([[1,2], [3,4]], dtype=float); v +- array([[ 1., 2.], +- [ 3., 4.]]) ++ array([[1., 2.], ++ [3., 4.]]) + sage: finance.TimeSeries(v) + [1.0000, 2.0000, 3.0000, 4.0000] + sage: finance.TimeSeries(v[:,0]) +@@ -2098,14 +2098,14 @@ cdef class TimeSeries: + + sage: w[0] = 20 + sage: w +- array([ 20. , -3. , 4.5, -2. ]) ++ array([20. , -3. , 4.5, -2. ]) + sage: v + [20.0000, -3.0000, 4.5000, -2.0000] + + If you want a separate copy do not give the ``copy=False`` option. :: + + sage: z = v.numpy(); z +- array([ 20. , -3. , 4.5, -2. ]) ++ array([20. , -3. , 4.5, -2. ]) + sage: z[0] = -10 + sage: v + [20.0000, -3.0000, 4.5000, -2.0000] +diff --git a/src/sage/functions/hyperbolic.py b/src/sage/functions/hyperbolic.py +index 931a4b41e4..bf33fc483d 100644 +--- a/src/sage/functions/hyperbolic.py ++++ b/src/sage/functions/hyperbolic.py +@@ -214,7 +214,7 @@ class Function_coth(GinacFunction): + sage: import numpy + sage: a = numpy.arange(2, 5) + sage: coth(a) +- array([ 1.03731472, 1.00496982, 1.00067115]) ++ array([1.03731472, 1.00496982, 1.00067115]) + """ + return 1.0 / tanh(x) + +@@ -267,7 +267,7 @@ class Function_sech(GinacFunction): + sage: import numpy + sage: a = numpy.arange(2, 5) + sage: sech(a) +- array([ 0.26580223, 0.09932793, 0.03661899]) ++ array([0.26580223, 0.09932793, 0.03661899]) + """ + return 1.0 / cosh(x) + +@@ -318,7 +318,7 @@ class Function_csch(GinacFunction): + sage: import numpy + sage: a = numpy.arange(2, 5) + sage: csch(a) +- array([ 0.27572056, 0.09982157, 0.03664357]) ++ array([0.27572056, 0.09982157, 0.03664357]) + """ + return 1.0 / sinh(x) + +@@ -586,7 +586,7 @@ class Function_arccoth(GinacFunction): + sage: import numpy + sage: a = numpy.arange(2,5) + sage: acoth(a) +- array([ 0.54930614, 0.34657359, 0.25541281]) ++ array([0.54930614, 0.34657359, 0.25541281]) + """ + return arctanh(1.0 / x) + +diff --git a/src/sage/functions/orthogonal_polys.py b/src/sage/functions/orthogonal_polys.py +index 017c85a96f..33fbb499c5 100644 +--- a/src/sage/functions/orthogonal_polys.py ++++ b/src/sage/functions/orthogonal_polys.py +@@ -810,12 +810,12 @@ class Func_chebyshev_T(ChebyshevFunction): + sage: z2 = numpy.array([[1,2],[1,2]]) + sage: z3 = numpy.array([1,2,3.]) + sage: chebyshev_T(1,z) +- array([ 1., 2.]) ++ array([1., 2.]) + sage: chebyshev_T(1,z2) +- array([[ 1., 2.], +- [ 1., 2.]]) ++ array([[1., 2.], ++ [1., 2.]]) + sage: chebyshev_T(1,z3) +- array([ 1., 2., 3.]) ++ array([1., 2., 3.]) + sage: chebyshev_T(z,0.1) + array([ 0.1 , -0.98]) + """ +@@ -1095,12 +1095,12 @@ class Func_chebyshev_U(ChebyshevFunction): + sage: z2 = numpy.array([[1,2],[1,2]]) + sage: z3 = numpy.array([1,2,3.]) + sage: chebyshev_U(1,z) +- array([ 2., 4.]) ++ array([2., 4.]) + sage: chebyshev_U(1,z2) +- array([[ 2., 4.], +- [ 2., 4.]]) ++ array([[2., 4.], ++ [2., 4.]]) + sage: chebyshev_U(1,z3) +- array([ 2., 4., 6.]) ++ array([2., 4., 6.]) + sage: chebyshev_U(z,0.1) + array([ 0.2 , -0.96]) + """ +diff --git a/src/sage/functions/other.py b/src/sage/functions/other.py +index 679384c907..d63b295a4c 100644 +--- a/src/sage/functions/other.py ++++ b/src/sage/functions/other.py +@@ -390,7 +390,7 @@ class Function_ceil(BuiltinFunction): + sage: import numpy + sage: a = numpy.linspace(0,2,6) + sage: ceil(a) +- array([ 0., 1., 1., 2., 2., 2.]) ++ array([0., 1., 1., 2., 2., 2.]) + + Test pickling:: + +@@ -539,7 +539,7 @@ class Function_floor(BuiltinFunction): + sage: import numpy + sage: a = numpy.linspace(0,2,6) + sage: floor(a) +- array([ 0., 0., 0., 1., 1., 2.]) ++ array([0., 0., 0., 1., 1., 2.]) + sage: floor(x)._sympy_() + floor(x) + +@@ -840,7 +840,7 @@ def sqrt(x, *args, **kwds): + sage: import numpy + sage: a = numpy.arange(2,5) + sage: sqrt(a) +- array([ 1.41421356, 1.73205081, 2. ]) ++ array([1.41421356, 1.73205081, 2. ]) + """ + if isinstance(x, float): + return math.sqrt(x) +diff --git a/src/sage/functions/trig.py b/src/sage/functions/trig.py +index e7e7a311cd..e7ff78a9de 100644 +--- a/src/sage/functions/trig.py ++++ b/src/sage/functions/trig.py +@@ -731,7 +731,7 @@ class Function_arccot(GinacFunction): + sage: import numpy + sage: a = numpy.arange(2, 5) + sage: arccot(a) +- array([ 0.46364761, 0.32175055, 0.24497866]) ++ array([0.46364761, 0.32175055, 0.24497866]) + """ + return math.pi/2 - arctan(x) + +@@ -787,7 +787,7 @@ class Function_arccsc(GinacFunction): + sage: import numpy + sage: a = numpy.arange(2, 5) + sage: arccsc(a) +- array([ 0.52359878, 0.33983691, 0.25268026]) ++ array([0.52359878, 0.33983691, 0.25268026]) + """ + return arcsin(1.0/x) + +@@ -845,7 +845,7 @@ class Function_arcsec(GinacFunction): + sage: import numpy + sage: a = numpy.arange(2, 5) + sage: arcsec(a) +- array([ 1.04719755, 1.23095942, 1.31811607]) ++ array([1.04719755, 1.23095942, 1.31811607]) + """ + return arccos(1.0/x) + +@@ -920,13 +920,13 @@ class Function_arctan2(GinacFunction): + sage: a = numpy.linspace(1, 3, 3) + sage: b = numpy.linspace(3, 6, 3) + sage: atan2(a, b) +- array([ 0.32175055, 0.41822433, 0.46364761]) ++ array([0.32175055, 0.41822433, 0.46364761]) + + sage: atan2(1,a) +- array([ 0.78539816, 0.46364761, 0.32175055]) ++ array([0.78539816, 0.46364761, 0.32175055]) + + sage: atan2(a, 1) +- array([ 0.78539816, 1.10714872, 1.24904577]) ++ array([0.78539816, 1.10714872, 1.24904577]) + + TESTS:: + +diff --git a/src/sage/matrix/constructor.pyx b/src/sage/matrix/constructor.pyx +index 19a1d37df0..5780dfae1c 100644 +--- a/src/sage/matrix/constructor.pyx ++++ b/src/sage/matrix/constructor.pyx +@@ -494,8 +494,8 @@ class MatrixFactory(object): + [7 8 9] + Full MatrixSpace of 3 by 3 dense matrices over Integer Ring + sage: n = matrix(QQ, 2, 2, [1, 1/2, 1/3, 1/4]).numpy(); n +- array([[ 1. , 0.5 ], +- [ 0.33333333, 0.25 ]]) ++ array([[1. , 0.5 ], ++ [0.33333333, 0.25 ]]) + sage: matrix(QQ, n) + [ 1 1/2] + [1/3 1/4] +diff --git a/src/sage/matrix/matrix_double_dense.pyx b/src/sage/matrix/matrix_double_dense.pyx +index 48e0a8a97f..1be5d35b19 100644 +--- a/src/sage/matrix/matrix_double_dense.pyx ++++ b/src/sage/matrix/matrix_double_dense.pyx +@@ -2546,7 +2546,7 @@ cdef class Matrix_double_dense(Matrix_dense): + sage: P.is_unitary(algorithm='orthonormal') + Traceback (most recent call last): + ... +- ValueError: failed to create intent(cache|hide)|optional array-- must have defined dimensions but got (0,) ++ error: ((lwork==-1)||(lwork >= MAX(1,2*n))) failed for 3rd keyword lwork: zgees:lwork=0 + + TESTS:: + +@@ -3662,8 +3662,8 @@ cdef class Matrix_double_dense(Matrix_dense): + [0.0 1.0 2.0] + [3.0 4.0 5.0] + sage: m.numpy() +- array([[ 0., 1., 2.], +- [ 3., 4., 5.]]) ++ array([[0., 1., 2.], ++ [3., 4., 5.]]) + + Alternatively, numpy automatically calls this function (via + the magic :meth:`__array__` method) to convert Sage matrices +@@ -3674,16 +3674,16 @@ cdef class Matrix_double_dense(Matrix_dense): + [0.0 1.0 2.0] + [3.0 4.0 5.0] + sage: numpy.array(m) +- array([[ 0., 1., 2.], +- [ 3., 4., 5.]]) ++ array([[0., 1., 2.], ++ [3., 4., 5.]]) + sage: numpy.array(m).dtype + dtype('float64') + sage: m = matrix(CDF, 2, range(6)); m + [0.0 1.0 2.0] + [3.0 4.0 5.0] + sage: numpy.array(m) +- array([[ 0.+0.j, 1.+0.j, 2.+0.j], +- [ 3.+0.j, 4.+0.j, 5.+0.j]]) ++ array([[0.+0.j, 1.+0.j, 2.+0.j], ++ [3.+0.j, 4.+0.j, 5.+0.j]]) + sage: numpy.array(m).dtype + dtype('complex128') + +diff --git a/src/sage/matrix/special.py b/src/sage/matrix/special.py +index c698ba5e97..b743bab354 100644 +--- a/src/sage/matrix/special.py ++++ b/src/sage/matrix/special.py +@@ -705,7 +705,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True): + + sage: import numpy + sage: entries = numpy.array([1.2, 5.6]); entries +- array([ 1.2, 5.6]) ++ array([1.2, 5.6]) + sage: A = diagonal_matrix(3, entries); A + [1.2 0.0 0.0] + [0.0 5.6 0.0] +@@ -715,7 +715,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True): + + sage: j = numpy.complex(0,1) + sage: entries = numpy.array([2.0+j, 8.1, 3.4+2.6*j]); entries +- array([ 2.0+1.j , 8.1+0.j , 3.4+2.6j]) ++ array([2. +1.j , 8.1+0.j , 3.4+2.6j]) + sage: A = diagonal_matrix(entries); A + [2.0 + 1.0*I 0.0 0.0] + [ 0.0 8.1 0.0] +diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx +index 230f142117..2ab1c0ae68 100644 +--- a/src/sage/modules/free_module_element.pyx ++++ b/src/sage/modules/free_module_element.pyx +@@ -982,7 +982,7 @@ cdef class FreeModuleElement(Vector): # abstract base class + sage: v.numpy() + array([1, 2, 5/6], dtype=object) + sage: v.numpy(dtype=float) +- array([ 1. , 2. , 0.83333333]) ++ array([1. , 2. , 0.83333333]) + sage: v.numpy(dtype=int) + array([1, 2, 0]) + sage: import numpy +@@ -993,7 +993,7 @@ cdef class FreeModuleElement(Vector): # abstract base class + be more efficient but may have unintended consequences:: + + sage: v.numpy(dtype=None) +- array([ 1. , 2. , 0.83333333]) ++ array([1. , 2. , 0.83333333]) + + sage: w = vector(ZZ, [0, 1, 2^63 -1]); w + (0, 1, 9223372036854775807) +diff --git a/src/sage/modules/vector_double_dense.pyx b/src/sage/modules/vector_double_dense.pyx +index 39fc2970de..2badf98284 100644 +--- a/src/sage/modules/vector_double_dense.pyx ++++ b/src/sage/modules/vector_double_dense.pyx +@@ -807,13 +807,13 @@ cdef class Vector_double_dense(FreeModuleElement): + + sage: v = vector(CDF,4,range(4)) + sage: v.numpy() +- array([ 0.+0.j, 1.+0.j, 2.+0.j, 3.+0.j]) ++ array([0.+0.j, 1.+0.j, 2.+0.j, 3.+0.j]) + sage: v = vector(CDF,0) + sage: v.numpy() + array([], dtype=complex128) + sage: v = vector(RDF,4,range(4)) + sage: v.numpy() +- array([ 0., 1., 2., 3.]) ++ array([0., 1., 2., 3.]) + sage: v = vector(RDF,0) + sage: v.numpy() + array([], dtype=float64) +@@ -823,11 +823,11 @@ cdef class Vector_double_dense(FreeModuleElement): + sage: import numpy + sage: v = vector(CDF, 3, range(3)) + sage: v.numpy() +- array([ 0.+0.j, 1.+0.j, 2.+0.j]) ++ array([0.+0.j, 1.+0.j, 2.+0.j]) + sage: v.numpy(dtype=numpy.float64) +- array([ 0., 1., 2.]) ++ array([0., 1., 2.]) + sage: v.numpy(dtype=numpy.float32) +- array([ 0., 1., 2.], dtype=float32) ++ array([0., 1., 2.], dtype=float32) + """ + if dtype is None or dtype is self._vector_numpy.dtype: + from copy import copy +diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py +index 17b5ebb84b..92ce35c502 100644 +--- a/src/sage/numerical/optimize.py ++++ b/src/sage/numerical/optimize.py +@@ -486,9 +486,9 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args) + else: + min = optimize.fmin_tnc(f, x0, approx_grad=True, bounds=cons, messages=0, **args)[0] + elif isinstance(cons[0], function_type) or isinstance(cons[0], Expression): +- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args) ++ min = optimize.fmin_cobyla(f, x0, cons, disp=0, **args) + elif isinstance(cons, function_type) or isinstance(cons, Expression): +- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args) ++ min = optimize.fmin_cobyla(f, x0, cons, disp=0, **args) + return vector(RDF, min) + + +diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx +index ad9693da62..758fb709b7 100644 +--- a/src/sage/plot/complex_plot.pyx ++++ b/src/sage/plot/complex_plot.pyx +@@ -61,9 +61,9 @@ cdef inline double mag_to_lightness(double r): + + sage: from sage.plot.complex_plot import complex_to_rgb + sage: complex_to_rgb([[0, 1, 10]]) +- array([[[ 0. , 0. , 0. ], +- [ 0.77172568, 0. , 0. ], +- [ 1. , 0.22134776, 0.22134776]]]) ++ array([[[0. , 0. , 0. ], ++ [0.77172568, 0. , 0. ], ++ [1. , 0.22134776, 0.22134776]]]) + """ + return atan(log(sqrt(r)+1)) * (4/PI) - 1 + +@@ -82,13 +82,13 @@ def complex_to_rgb(z_values): + + sage: from sage.plot.complex_plot import complex_to_rgb + sage: complex_to_rgb([[0, 1, 1000]]) +- array([[[ 0. , 0. , 0. ], +- [ 0.77172568, 0. , 0. ], +- [ 1. , 0.64421177, 0.64421177]]]) ++ array([[[0. , 0. , 0. ], ++ [0.77172568, 0. , 0. ], ++ [1. , 0.64421177, 0.64421177]]]) + sage: complex_to_rgb([[0, 1j, 1000j]]) +- array([[[ 0. , 0. , 0. ], +- [ 0.38586284, 0.77172568, 0. ], +- [ 0.82210588, 1. , 0.64421177]]]) ++ array([[[0. , 0. , 0. ], ++ [0.38586284, 0.77172568, 0. ], ++ [0.82210588, 1. , 0.64421177]]]) + """ + import numpy + cdef unsigned int i, j, imax, jmax +diff --git a/src/sage/plot/line.py b/src/sage/plot/line.py +index 23f5e61446..3b1b51d7cf 100644 +--- a/src/sage/plot/line.py ++++ b/src/sage/plot/line.py +@@ -502,14 +502,12 @@ def line2d(points, **options): + from sage.plot.all import Graphics + from sage.plot.plot import xydata_from_point_list + from sage.rings.all import CC, CDF ++ points = list(points) # make sure points is a python list + if points in CC or points in CDF: + pass + else: +- try: +- if not points: +- return Graphics() +- except ValueError: # numpy raises a ValueError if not empty +- pass ++ if len(points) == 0: ++ return Graphics() + xdata, ydata = xydata_from_point_list(points) + g = Graphics() + g._set_extra_kwds(Graphics._extract_kwds_for_show(options)) +diff --git a/src/sage/plot/plot_field.py b/src/sage/plot/plot_field.py +index 0025098a8d..23c80902f3 100644 +--- a/src/sage/plot/plot_field.py ++++ b/src/sage/plot/plot_field.py +@@ -49,9 +49,10 @@ class PlotField(GraphicPrimitive): + sage: r.xpos_array + [0.0, 0.0, 1.0, 1.0] + sage: r.yvec_array +- masked_array(data = [0.0 0.70710678118... 0.70710678118... 0.89442719...], +- mask = [False False False False], +- fill_value = 1e+20) ++ masked_array(data=[0.0, 0.70710678118..., 0.70710678118..., ++ 0.89442719...], ++ mask=[False, False, False, False], ++ fill_value=1e+20) + + TESTS: + +diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py +index f3da57c370..3806f4b32f 100644 +--- a/src/sage/plot/streamline_plot.py ++++ b/src/sage/plot/streamline_plot.py +@@ -38,16 +38,14 @@ class StreamlinePlot(GraphicPrimitive): + sage: r.options()['plot_points'] + 2 + sage: r.xpos_array +- array([ 0., 1.]) ++ array([0., 1.]) + sage: r.yvec_array +- masked_array(data = +- [[1.0 1.0] +- [0.5403023058681398 0.5403023058681398]], +- mask = +- [[False False] +- [False False]], +- fill_value = 1e+20) +- ++ masked_array( ++ data=[[1.0, 1.0], ++ [0.5403023058681398, 0.5403023058681398]], ++ mask=[[False, False], ++ [False, False]], ++ fill_value=1e+20) + + TESTS: + +diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx +index f66cd898b9..35995886d5 100644 +--- a/src/sage/probability/probability_distribution.pyx ++++ b/src/sage/probability/probability_distribution.pyx +@@ -130,7 +130,17 @@ cdef class ProbabilityDistribution: + 0.0, + 1.4650000000000003] + sage: b +- [0.0, 0.20000000000000001, 0.40000000000000002, 0.60000000000000009, 0.80000000000000004, 1.0, 1.2000000000000002, 1.4000000000000001, 1.6000000000000001, 1.8, 2.0] ++ [0.0, ++ 0.2, ++ 0.4, ++ 0.6000000000000001, ++ 0.8, ++ 1.0, ++ 1.2000000000000002, ++ 1.4000000000000001, ++ 1.6, ++ 1.8, ++ 2.0] + """ + import pylab + l = [float(self.get_random_element()) for _ in range(num_samples)] +diff --git a/src/sage/rings/rational.pyx b/src/sage/rings/rational.pyx +index a0bfe080f5..7d95e7a1a8 100644 +--- a/src/sage/rings/rational.pyx ++++ b/src/sage/rings/rational.pyx +@@ -1056,7 +1056,7 @@ cdef class Rational(sage.structure.element.FieldElement): + dtype('O') + + sage: numpy.array([1, 1/2, 3/4]) +- array([ 1. , 0.5 , 0.75]) ++ array([1. , 0.5 , 0.75]) + """ + if mpz_cmp_ui(mpq_denref(self.value), 1) == 0: + if mpz_fits_slong_p(mpq_numref(self.value)): +diff --git a/src/sage/rings/real_mpfr.pyx b/src/sage/rings/real_mpfr.pyx +index 4c630867a4..64e2187f5b 100644 +--- a/src/sage/rings/real_mpfr.pyx ++++ b/src/sage/rings/real_mpfr.pyx +@@ -1438,7 +1438,7 @@ cdef class RealNumber(sage.structure.element.RingElement): + + sage: import numpy + sage: numpy.arange(10.0) +- array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.]) ++ array([0., 1., 2., 3., 4., 5., 6., 7., 8., 9.]) + sage: numpy.array([1.0, 1.1, 1.2]).dtype + dtype('float64') + sage: numpy.array([1.000000000000000000000000000000000000]).dtype +diff --git a/src/sage/schemes/elliptic_curves/height.py b/src/sage/schemes/elliptic_curves/height.py +index 3d270ebf9d..1144f168e3 100644 +--- a/src/sage/schemes/elliptic_curves/height.py ++++ b/src/sage/schemes/elliptic_curves/height.py +@@ -1623,18 +1623,18 @@ class EllipticCurveCanonicalHeight: + even:: + + sage: H.wp_on_grid(v,4) +- array([[ 25.43920182, 5.28760943, 5.28760943, 25.43920182], +- [ 6.05099485, 1.83757786, 1.83757786, 6.05099485], +- [ 6.05099485, 1.83757786, 1.83757786, 6.05099485], +- [ 25.43920182, 5.28760943, 5.28760943, 25.43920182]]) ++ array([[25.43920182, 5.28760943, 5.28760943, 25.43920182], ++ [ 6.05099485, 1.83757786, 1.83757786, 6.05099485], ++ [ 6.05099485, 1.83757786, 1.83757786, 6.05099485], ++ [25.43920182, 5.28760943, 5.28760943, 25.43920182]]) + + The array of values on the half-grid:: + + sage: H.wp_on_grid(v,4,True) +- array([[ 25.43920182, 5.28760943], +- [ 6.05099485, 1.83757786], +- [ 6.05099485, 1.83757786], +- [ 25.43920182, 5.28760943]]) ++ array([[25.43920182, 5.28760943], ++ [ 6.05099485, 1.83757786], ++ [ 6.05099485, 1.83757786], ++ [25.43920182, 5.28760943]]) + """ + tau = self.tau(v) + fk, err = self.fk_intervals(v, 15, CDF) +diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx +index 2dcb0492b9..2b1a06385c 100644 +--- a/src/sage/symbolic/ring.pyx ++++ b/src/sage/symbolic/ring.pyx +@@ -1135,7 +1135,7 @@ cdef class NumpyToSRMorphism(Morphism): + sage: cos(numpy.int('2')) + cos(2) + sage: numpy.cos(numpy.int('2')) +- -0.41614683654714241 ++ -0.4161468365471424 + """ + cdef _intermediate_ring + diff --git a/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch b/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch new file mode 100644 index 000000000000..49cdfd189b92 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch @@ -0,0 +1,20 @@ +diff --git a/src/sage/doctest/parsing.py b/src/sage/doctest/parsing.py +index 6bdc9a0..31fc780 100644 +--- a/src/sage/doctest/parsing.py ++++ b/src/sage/doctest/parsing.py +@@ -40,6 +40,7 @@ from .external import available_software + + float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)') + optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))') ++pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.') + find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M) + find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M) + random_marker = re.compile('.*random', re.I) +@@ -935,6 +936,7 @@ class SageOutputChecker(doctest.OutputChecker): + + """ + got = self.human_readable_escape_sequences(got) ++ got = pari_stack_warning_regex.sub('', got) + if isinstance(want, MarkedOutput): + if want.random: + return True diff --git a/pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch b/pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch new file mode 100644 index 000000000000..22f274d608d4 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch @@ -0,0 +1,479 @@ +diff --git a/src/sage/calculus/calculus.py b/src/sage/calculus/calculus.py +index 3a417d9d5c..fadaadbaf6 100644 +--- a/src/sage/calculus/calculus.py ++++ b/src/sage/calculus/calculus.py +@@ -231,7 +231,7 @@ Another example:: + sage: f(x=3) + arcsinh(1) + sage: f.derivative(x) +- 1/3/sqrt(1/9*x^2 + 1) ++ 1/sqrt(x^2 + 9) + + We compute the length of the parabola from 0 to 2:: + +@@ -1509,8 +1509,8 @@ def laplace(ex, t, s, algorithm='maxima'): + Testing SymPy:: + + sage: laplace(t^n, t, s, algorithm='sympy') +- (s^(-n)*gamma(n + 1)/s, 0, -re(n) < 1) +- ++ (gamma(n + 1)/(s*s^n), 0, -re(n) < 1) ++ + Testing Maxima:: + + sage: laplace(t^n, t, s, algorithm='maxima') +diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py +index 1fc2db5c94..f3e49b9cdb 100644 +--- a/src/sage/functions/hypergeometric.py ++++ b/src/sage/functions/hypergeometric.py +@@ -34,7 +34,7 @@ Simplification (note that ``simplify_full`` does not yet call + sage: a.simplify_hypergeometric() + 1/((-e^x + 1)^e^x) + sage: a.simplify_hypergeometric(algorithm='sage') +- (-e^x + 1)^(-e^x) ++ 1/((-e^x + 1)^e^x) + + Equality testing:: + +@@ -145,7 +145,7 @@ Series expansions of confluent hypergeometric functions:: + + sage: hypergeometric_M(2, 2, x).series(x, 3) + 1 + 1*x + 1/2*x^2 + Order(x^3) +- sage: hypergeometric_U(2, 2, x).series(x == 3, 100).subs(x=1).n() ++ sage: hypergeometric_U(2, 2, x).series(x == 3, 100).subs(x=1).n() # known bug (see :trac:`25688`) + 0.403652637676806 + sage: hypergeometric_U(2, 2, 1).n() + 0.403652637676806 +@@ -773,7 +773,7 @@ def closed_form(hyp): + sage: closed_form(hypergeometric([], [], z)) + e^z + sage: closed_form(hypergeometric([a], [], z)) +- (-z + 1)^(-a) ++ 1/((-z + 1)^a) + sage: closed_form(hypergeometric([1, 1, 2], [1, 1], z)) + (z - 1)^(-2) + sage: closed_form(hypergeometric([2, 3], [1], x)) +@@ -1121,7 +1121,7 @@ class Hypergeometric_U(BuiltinFunction): + sage: var('a b z') + (a, b, z) + sage: hypergeometric_U(a, b, z).generalized() +- z^(-a)*hypergeometric((a, a - b + 1), (), -1/z) ++ hypergeometric((a, a - b + 1), (), -1/z)/z^a + sage: hypergeometric_U(1, 3, 1/2).generalized() + 2*hypergeometric((1, -1), (), -2) + sage: hypergeometric_U(3, I, 2).generalized() +diff --git a/src/sage/functions/log.py b/src/sage/functions/log.py +index 75d1bf8060..61968582af 100644 +--- a/src/sage/functions/log.py ++++ b/src/sage/functions/log.py +@@ -518,17 +518,17 @@ class Function_polylog(GinacFunction): + + sage: BF = RealBallField(100) + sage: polylog(2, BF(1/3)) +- [0.36621322997706348761674629766 +/- 4.51e-30] ++ [0.36621322997706348761674629766... +/- ...] + sage: polylog(2, BF(4/3)) +- nan ++ [2.27001825336107090380391448586 +/- 5.64e-30] + [-0.90377988538400159956755721265 +/- 8.39e-30]*I + sage: parent(_) +- Real ball field with 100 bits of precision ++ Complex ball field with 100 bits of precision + sage: polylog(2, CBF(1/3)) +- [0.366213229977063 +/- 5.85e-16] ++ [0.366213229977063 +/- ...] + sage: parent(_) + Complex ball field with 53 bits of precision + sage: polylog(2, CBF(1)) +- [1.644934066848226 +/- 6.59e-16] ++ [1.644934066848226 +/- ...] + sage: parent(_) + Complex ball field with 53 bits of precision + """ +diff --git a/src/sage/functions/trig.py b/src/sage/functions/trig.py +index e7e7a311cd..1f2926d6c9 100644 +--- a/src/sage/functions/trig.py ++++ b/src/sage/functions/trig.py +@@ -529,13 +529,8 @@ class Function_arcsin(GinacFunction): + arcsin + sage: asin(complex(1,1)) + (0.6662394324925152+1.0612750619050357j) +- +- Check that :trac:`22823` is fixed:: +- +- sage: bool(asin(SR(2.1)) == NaN) +- True +- sage: asin(SR(2.1)).is_real() +- False ++ sage: asin(SR(2.1)) ++ 1.57079632679490 - 1.37285914424258*I + """ + GinacFunction.__init__(self, 'arcsin', latex_name=r"\arcsin", + conversions=dict(maxima='asin', sympy='asin', fricas="asin", giac="asin")) +@@ -595,13 +590,8 @@ class Function_arccos(GinacFunction): + arccos + sage: acos(complex(1,1)) + (0.9045568943023814-1.0612750619050357j) +- +- Check that :trac:`22823` is fixed:: +- +- sage: bool(acos(SR(2.1)) == NaN) +- True +- sage: acos(SR(2.1)).is_real() +- False ++ sage: acos(SR(2.1)) ++ 1.37285914424258*I + """ + GinacFunction.__init__(self, 'arccos', latex_name=r"\arccos", + conversions=dict(maxima='acos', sympy='acos', fricas='acos', giac='acos')) +@@ -807,7 +797,7 @@ class Function_arcsec(GinacFunction): + sage: arcsec(2).n(100) + 1.0471975511965977461542144611 + sage: arcsec(1/2).n(100) +- NaN ++ 1.3169578969248167086250463473*I + sage: RDF(arcsec(2)) # abs tol 1e-15 + 1.0471975511965976 + sage: arcsec(1 + I) +@@ -958,7 +948,9 @@ class Function_arctan2(GinacFunction): + sage: atan2(0,0,hold=True) + arctan2(0, 0) + sage: atan2(0,0,hold=True).n() +- NaN ++ Traceback (most recent call last): ++ ... ++ RuntimeError: atan2(): division by zero + + Check if :trac:`10062` is fixed, this was caused by + ``(I*I).is_positive()`` returning ``True``:: +diff --git a/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py b/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py +index 3b5c8d1729..1c6b73a16c 100644 +--- a/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py ++++ b/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py +@@ -1422,8 +1422,10 @@ class HyperbolicGeodesicUHP(HyperbolicGeodesic): + expressions do not generate runtime errors. :: + + sage: g=HyperbolicPlane().UHP().get_geodesic(-1+I,1+I) +- sage: g.midpoint() +- Point in UHP 1/2*(sqrt(2)*e^(1/2*arccosh(3)) - sqrt(2) + (I - 1)*e^(1/2*arccosh(3)) + I - 1)/((1/4*I - 1/4)*sqrt(2)*e^(1/2*arccosh(3)) - (1/4*I - 1/4)*sqrt(2) + 1/2*e^(1/2*arccosh(3)) + 1/2) ++ sage: point = g.midpoint(); point ++ Point in UHP -1/2*(sqrt(2)*... ++ sage: QQbar(point.coordinates()).radical_expression() ++ I*sqrt(2) + + Check that floating points remain floating points + in :meth:`midpoint` :: +diff --git a/src/sage/interfaces/fricas.py b/src/sage/interfaces/fricas.py +index 82aae78e37..8501ea2a18 100644 +--- a/src/sage/interfaces/fricas.py ++++ b/src/sage/interfaces/fricas.py +@@ -1084,14 +1084,14 @@ class FriCASElement(ExpectElement): + 0.451026811796262, + 0.732815101786507, + 0.837981225008390, +- NaN, +- NaN, ++ 1.57079632679490 - 0.467145308103262*I, ++ 0.467145308103262*I, + 1.11976951499863, + 0.451026811796262, + 0.732815101786507, + 0.837981225008390, +- NaN, +- NaN] ++ 1.57079632679490 - 0.467145308103262*I, ++ 0.467145308103262*I] + sage: l = [tanh, sinh, cosh, coth, sech, csch, asinh, acosh, atanh, acoth, asech, acsch, arcsinh, arccosh, arctanh, arccoth, arcsech, arccsch] + sage: [f(x)._fricas_().sage().subs(x=0.9) for f in l] # optional - fricas + [0.716297870199024, +diff --git a/src/sage/libs/pynac/pynac.pyx b/src/sage/libs/pynac/pynac.pyx +index 9e9d8f664b..e3406f007e 100644 +--- a/src/sage/libs/pynac/pynac.pyx ++++ b/src/sage/libs/pynac/pynac.pyx +@@ -1824,7 +1824,7 @@ cdef py_atan2(x, y): + sage: atan2(CC(I), CC(I+1)) + 0.553574358897045 + 0.402359478108525*I + sage: atan2(CBF(I), CBF(I+1)) +- [0.55357435889705 +/- 5.58e-15] + [0.402359478108525 +/- 7.11e-16]*I ++ [0.55357435889705 +/- ...] + [0.402359478108525 +/- ...]*I + + Check that :trac:`23776` is fixed and RDF input gives real output:: + +diff --git a/src/sage/matrix/matrix_symbolic_dense.pyx b/src/sage/matrix/matrix_symbolic_dense.pyx +index 46a15e53eb..7a0beb437b 100644 +--- a/src/sage/matrix/matrix_symbolic_dense.pyx ++++ b/src/sage/matrix/matrix_symbolic_dense.pyx +@@ -200,7 +200,7 @@ cdef class Matrix_symbolic_dense(Matrix_generic_dense): + sage: eval, [evec], mult = es[0] + sage: delta = eval*evec - evec*A + sage: abs(abs(delta)) < 1e-10 +- sqrt(9/25*((2*sqrt(6) - 3)*(sqrt(6) - 2) + 7*sqrt(6) - 18)^2 + 9/25*((sqrt(6) - 2)*(sqrt(6) - 4) + 6*sqrt(6) - 14)^2) < (1.00000000000000e-10) ++ 3/5*sqrt(((2*sqrt(6) - 3)*(sqrt(6) - 2) + 7*sqrt(6) - 18)^2 + ((sqrt(6) - 2)*(sqrt(6) - 4) + 6*sqrt(6) - 14)^2) < (1.00000000000000e-10) + sage: abs(abs(delta)).n() < 1e-10 + True + +diff --git a/src/sage/modules/matrix_morphism.py b/src/sage/modules/matrix_morphism.py +index 17a1d6e290..03892ceec0 100644 +--- a/src/sage/modules/matrix_morphism.py ++++ b/src/sage/modules/matrix_morphism.py +@@ -214,9 +214,9 @@ class MatrixMorphism_abstract(sage.categories.morphism.Morphism): + sage: f((1, 0)) + Traceback (most recent call last): + ... +- TypeError: Unable to coerce entries (=[1.00000000000000*I, 0.000000000000000]) to coefficients in Real Field with 53 bits of precision ++ TypeError: Unable to coerce entries (=[1.00000000000000*I, 0]) to coefficients in Real Field with 53 bits of precision + sage: f((1, 0), coerce=False) +- (1.00000000000000*I, 0.000000000000000) ++ (1.00000000000000*I, 0) + + """ + if self.domain().is_ambient(): +diff --git a/src/sage/plot/plot.py b/src/sage/plot/plot.py +index 77cdeb8c46..e501e74036 100644 +--- a/src/sage/plot/plot.py ++++ b/src/sage/plot/plot.py +@@ -2061,7 +2061,7 @@ def _plot(funcs, xrange, parametric=False, + plot properly (:trac:`13246`):: + + sage: parametric_plot((x, arcsec(x)), (x, -2, 2)) +- Graphics object consisting of 1 graphics primitive ++ Graphics object consisting of 2 graphics primitives + + """ + from sage.plot.colors import Color +diff --git a/src/sage/repl/display/formatter.py b/src/sage/repl/display/formatter.py +index 8ce2e839d7..948207c95e 100644 +--- a/src/sage/repl/display/formatter.py ++++ b/src/sage/repl/display/formatter.py +@@ -25,11 +25,11 @@ generally, all sage expression as an ASCII art object:: + sage: shell = get_test_shell() + sage: shell.run_cell('%display ascii_art') + sage: shell.run_cell('integral(x^2/pi^x, x)') +- / 2 2 \ -x*log(pi) +- -\x *log (pi) + 2*x*log(pi) + 2/*e +- --------------------------------------------- +- 3 +- log (pi) ++ -x / 2 2 \ ++ -pi *\x *log (pi) + 2*x*log(pi) + 2/ ++ -------------------------------------- ++ 3 ++ log (pi) + sage: shell.run_cell("i = var('i')") + sage: shell.run_cell('sum(i*x^i, i, 0, 10)') + 10 9 8 7 6 5 4 3 2 +diff --git a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py +index d8ebbf4f76..8c60f65e99 100644 +--- a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py ++++ b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py +@@ -151,8 +151,8 @@ A multiple point example (Example 6.5 of [RaWi2012]_):: + [(x + 2*y - 1, 1), (2*x + y - 1, 1)]) + sage: F1 = decomp[1] + sage: F1.asymptotics(p, alpha, 2) +- (-3*((2*a^2 - 5*a*b + 2*b^2)*r^2 + (a + b)*r + 3)*((1/3)^(-a)*(1/3)^(-b))^r, +- (1/3)^(-a)*(1/3)^(-b), -3*(2*a^2 - 5*a*b + 2*b^2)*r^2 - 3*(a + b)*r - 9) ++ (-3*((2*a^2 - 5*a*b + 2*b^2)*r^2 + (a + b)*r + 3)*(1/((1/3)^a*(1/3)^b))^r, ++ 1/((1/3)^a*(1/3)^b), -3*(2*a^2 - 5*a*b + 2*b^2)*r^2 - 3*(a + b)*r - 9) + sage: alpha = [4, 3] + sage: decomp = F.asymptotic_decomposition(alpha) + sage: F1 = decomp[1] +@@ -2159,7 +2159,7 @@ class FractionWithFactoredDenominator(RingElement): + sage: p = {x: 1/3, y: 1/3} + sage: alpha = (var('a'), var('b')) + sage: F.asymptotics_multiple(p, alpha, 2, var('r')) # long time +- (3*((1/3)^(-a)*(1/3)^(-b))^r*e^(2/3), (1/3)^(-a)*(1/3)^(-b), 3*e^(2/3)) ++ (3*(1/((1/3)^a*(1/3)^b))^r*e^(2/3), 1/((1/3)^a*(1/3)^b), 3*e^(2/3)) + """ + from itertools import product + from sage.calculus.functions import jacobian +diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py +index 16a268a02c..5fd244e93b 100644 +--- a/src/sage/stats/basic_stats.py ++++ b/src/sage/stats/basic_stats.py +@@ -183,7 +183,7 @@ def std(v, bias=False): + sage: std([]) + NaN + sage: std([I, sqrt(2), 3/5]) +- sqrt(1/450*(10*sqrt(2) - 5*I - 3)^2 + 1/450*(5*sqrt(2) - 10*I + 3)^2 + 1/450*(5*sqrt(2) + 5*I - 6)^2) ++ 1/15*sqrt(1/2)*sqrt((10*sqrt(2) - 5*I - 3)^2 + (5*sqrt(2) - 10*I + 3)^2 + (5*sqrt(2) + 5*I - 6)^2) + sage: std([RIF(1.0103, 1.0103), RIF(2)]) + 0.6998235813403261? + sage: import numpy +diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx +index ab4c05de3a..60f0dc549a 100644 +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -622,7 +622,7 @@ cdef class Expression(CommutativeRingElement): + sage: x^(-5) + x^(-5) + sage: x^(-y) +- x^(-y) ++ 1/(x^y) + sage: 2*x^(-1) + 2/x + sage: i*x +@@ -3621,14 +3621,14 @@ cdef class Expression(CommutativeRingElement): + sage: repl_dict = {b_0: b_0, b_3: b_1, b_2: b_3, b_1: b_2} + sage: P = precomp.substitute(repl_dict) + sage: P.expand() +- -2^(-b_0)*2^(-b_2)*2^b_3 - 2^b_0*2^(-b_2)*2^b_3 - +- 2^(-b_0)*2^b_2*2^b_3 + 2^b_0*2^b_2*2^b_3 - 2*2^(-b_0)*2^(-b_2) +- - 2*2^b_0*2^(-b_2) - 2*2^(-b_0)*2^b_2 + 2*2^b_0*2^b_2 + +- 2^(-b_0)*2^b_3 + 2^b_0*2^b_3 + 2^(-b_2)*2^b_3 + 2^b_2*2^b_3 + +- 2*2^(-b_0) + 2*2^b_0 + 2*2^(-b_2) + 2*2^b_2 - 9*2^b_3 - +- 2^(-b_0)*2^(-b_2)/2^b_3 - 2^b_0*2^(-b_2)/2^b_3 - +- 2^(-b_0)*2^b_2/2^b_3 + 2^b_0*2^b_2/2^b_3 + 2^(-b_0)/2^b_3 + +- 2^b_0/2^b_3 + 2^(-b_2)/2^b_3 + 2^b_2/2^b_3 - 9/2^b_3 - 18 ++ 2^b_0*2^b_2*2^b_3 + 2*2^b_0*2^b_2 + 2^b_0*2^b_3 + 2^b_2*2^b_3 + ++ 2*2^b_0 + 2*2^b_2 - 9*2^b_3 + 2^b_0*2^b_2/2^b_3 - ++ 2^b_0*2^b_3/2^b_2 - 2^b_2*2^b_3/2^b_0 - 2*2^b_0/2^b_2 - ++ 2*2^b_2/2^b_0 + 2^b_0/2^b_3 + 2^b_2/2^b_3 + 2^b_3/2^b_0 + ++ 2^b_3/2^b_2 + 2/2^b_0 + 2/2^b_2 - 2^b_0/(2^b_2*2^b_3) - ++ 2^b_2/(2^b_0*2^b_3) - 9/2^b_3 - 2^b_3/(2^b_0*2^b_2) - ++ 2/(2^b_0*2^b_2) + 1/(2^b_0*2^b_3) + 1/(2^b_2*2^b_3) - ++ 1/(2^b_0*2^b_2*2^b_3) - 18 + + sage: _0,b_1,b_2=var('b_0,b_1,b_2') + sage: f = 1/27*b_2^2/(2^b_2)^2 + 1/27*b_1^2/(2^b_1)^2 + \ +@@ -3809,7 +3809,7 @@ cdef class Expression(CommutativeRingElement): + + sage: x = SR.symbol('x', domain='real') + sage: (x^3)^(1/3) +- (x^3)^(1/3) ++ x + sage: (x^4)^(1/4) + abs(x) + sage: (x^8)^(1/4) +@@ -3872,7 +3872,7 @@ cdef class Expression(CommutativeRingElement): + sage: 2^(x/log(2)) + e^x + sage: 2^(-x^2/2/log(2)) +- e^(-1/2*x^2) ++ 1/e^(1/2*x^2) + sage: x^(x/log(x)) + x^(x/log(x)) + sage: assume(x > 0) +@@ -4816,18 +4816,24 @@ cdef class Expression(CommutativeRingElement): + sage: ((x+y)^(x+y)).match(w0^w0) + {$0: x + y} + sage: t = ((a+b)*(a+c)).match((a+w0)*(a+w1)) +- sage: t[w0], t[w1] +- (c, b) ++ sage: set([t[w0], t[w1]]) == set([b, c]) ++ True + sage: ((a+b)*(a+c)).match((w0+b)*(w0+c)) + {$0: a} + sage: t = ((a+b)*(a+c)).match((w0+w1)*(w0+w2)) +- sage: t[w0], t[w1], t[w2] +- (a, c, b) +- sage: print(((a+b)*(a+c)).match((w0+w1)*(w1+w2))) +- None ++ sage: t[w0] ++ a ++ sage: set([t[w1], t[w2]]) == set([b, c]) ++ True ++ sage: t = ((a+b)*(a+c)).match((w0+w1)*(w1+w2)) ++ sage: t[w1] ++ a ++ sage: set([t[w0], t[w2]]) == set([b, c]) ++ True + sage: t = (a*(x+y)+a*z+b).match(a*w0+w1) +- sage: t[w0], t[w1] +- (x + y, a*z + b) ++ sage: s = set([t[w0], t[w1]]) ++ sage: s == set([x+y, a*z+b]) or s == set([z, a*(x+y)+b]) ++ True + sage: print((a+b+c+d+f+g).match(c)) + None + sage: (a+b+c+d+f+g).has(c) +@@ -4836,7 +4842,7 @@ cdef class Expression(CommutativeRingElement): + {$0: a + b + d + f + g} + sage: (a+b+c+d+f+g).match(c+g+w0) + {$0: a + b + d + f} +- sage: (a+b).match(a+b+w0) ++ sage: (a+b).match(a+b+w0) # known bug + {$0: 0} + sage: print((a*b^2).match(a^w0*b^w1)) + None +@@ -5009,7 +5015,7 @@ cdef class Expression(CommutativeRingElement): + a^3 + b^3 + (x + y)^3 + + sage: t.subs(w0 == w0^2) +- (x^2 + y^2)^18 + a^16 + b^16 ++ a^8 + b^8 + (x^2 + y^2)^6 + + sage: t.subs(a == b, b == c) + (x + y)^3 + b^2 + c^2 +@@ -8392,9 +8398,13 @@ cdef class Expression(CommutativeRingElement): + sage: SR(I).arctan2(1) + arctan2(I, 1) + sage: SR(CDF(0,1)).arctan2(1) +- NaN + +infinity*I +- sage: SR(1).arctan2(CDF(0,1)) # known bug +- 0.7853981633974484 - 19.012501686914433*I ++ Traceback (most recent call last): ++ ... ++ ValueError: power::eval(): division by zero ++ sage: SR(1).arctan2(CDF(0,1)) ++ Traceback (most recent call last): ++ ... ++ ValueError: power::eval(): division by zero + + sage: arctan2(0,oo) + 0 +@@ -8656,7 +8666,7 @@ cdef class Expression(CommutativeRingElement): + 1/2*I*pi + sage: SR(1/2).arccosh() + arccosh(1/2) +- sage: SR(CDF(1/2)).arccosh() # rel tol 1e-15 ++ sage: SR(CDF(1/2)).arccosh() # rel tol 1e-15 + 1.0471975511965976*I + sage: maxima('acosh(0.5)') + 1.04719755119659...*%i +@@ -11687,7 +11697,7 @@ cdef class Expression(CommutativeRingElement): + sage: a.solve(t) + [] + sage: b = a.canonicalize_radical(); b +- -23040.0*(-2.0*e^(1800*t) + 25.0*e^(900*t) - 32.0)*e^(-2400*t) ++ (46080.0*e^(1800*t) - 576000.0*e^(900*t) + 737280.0)*e^(-2400*t) + sage: b.solve(t) + [] + sage: b.solve(t, to_poly_solve=True) +@@ -12163,14 +12173,14 @@ cdef class Expression(CommutativeRingElement): + + sage: (n,k,j)=var('n,k,j') + sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) +- -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) ++ -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) + sage: assume(j>-1) + sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) + 1 + sage: forget() + sage: assume(n>=j) + sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) +- -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) ++ -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) + sage: forget() + sage: assume(j==-1) + sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) +@@ -12178,7 +12188,7 @@ cdef class Expression(CommutativeRingElement): + sage: forget() + sage: assume(j<-1) + sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) +- -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) ++ -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) + sage: forget() + + Check that :trac:`16176` is fixed:: +diff --git a/src/sage/symbolic/relation.py b/src/sage/symbolic/relation.py +index da6f0eef42..4bd65ef572 100644 +--- a/src/sage/symbolic/relation.py ++++ b/src/sage/symbolic/relation.py +@@ -895,7 +895,7 @@ def solve(f, *args, **kwds): + sage: (r[0][x], r[0][y]) + (2*lambert_w(1/2), 1) + sage: solve(-2*x**3 + 4*x**2 - 2*x + 6 > 0, x, algorithm='sympy') +- [x < (1/6*sqrt(77) + 79/54)^(1/3) + 1/9/(1/6*sqrt(77) + 79/54)^(1/3) + 2/3] ++ [x < 1/3*(1/2)^(1/3)*(9*sqrt(77) + 79)^(1/3) + 2/3*(1/2)^(2/3)/(9*sqrt(77) + 79)^(1/3) + 2/3] + sage: solve(sqrt(2*x^2 - 7) - (3 - x),x,algorithm='sympy') + [x == -8, x == 2] + sage: solve(sqrt(2*x + 9) - sqrt(x + 1) - sqrt(x + 4),x,algorithm='sympy') diff --git a/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch b/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch new file mode 100644 index 000000000000..1b64f39fe60f --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch @@ -0,0 +1,28 @@ +diff --git a/src/sage/all.py b/src/sage/all.py +index ca309ef..be3186b 100644 +--- a/src/sage/all.py ++++ b/src/sage/all.py +@@ -298,6 +298,23 @@ warnings.filterwarnings('ignore', module='matplotlib[.]font_manager') + warnings.filterwarnings('default', + '[\s\S]*See http://trac.sagemath.org/[0-9]* for details.') + ++# Hotpatch around https://bugs.python.org/issue5755 which won't be fixed for ++# python 2.7. Idea by https://stackoverflow.com/a/36293331. ++from distutils.command.build_ext import build_ext ++from distutils.sysconfig import customize_compiler ++ ++_build_extensions = build_ext.build_extensions ++ ++def build_extensions_patched(self): ++ customize_compiler(self.compiler) ++ try: ++ self.compiler.compiler_so.remove("-Wstrict-prototypes") ++ except (AttributeError, ValueError): ++ pass ++ _build_extensions(self) ++ ++build_ext.build_extensions = build_extensions_patched ++ + + # Set a new random number seed as the very last thing + # (so that printing initial_seed() and using that seed diff --git a/pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch b/pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch new file mode 100644 index 000000000000..ff1dcd22acf3 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch @@ -0,0 +1,40 @@ +diff --git a/src/sage/tests/py3_syntax.py b/src/sage/tests/py3_syntax.py +index e564860b48..86ab3725f9 100644 +--- a/src/sage/tests/py3_syntax.py ++++ b/src/sage/tests/py3_syntax.py +@@ -179,15 +179,30 @@ class Python3SyntaxTest(SortedDirectoryWalkerABC): + sage: py3_syntax = Python3SyntaxTest() + sage: py3_syntax.test(src.name) + Invalid Python 3 syntax found: +- File "...py", line 1 +- print "invalid print statement" +- ^ +- SyntaxError: Missing parentheses in call to 'print' ++ Missing parentheses in call to 'print'... + sage: os.unlink(src.name) + """ ++ ++ # compile all given files in memory, printing all errors ++ # inspired by the py_compile module (but without writing to file) ++ script = """ ++import sys ++import importlib.machinery ++rv = 0 ++for file in sys.argv[1:]: ++ loader = importlib.machinery.SourceFileLoader('', file) ++ source_bytes = loader.get_data(file) ++ try: ++ code = loader.source_to_code(source_bytes, file) ++ except Exception as err: ++ print(err) ++ rv = 1 ++sys.exit(rv) ++""" + cmd = [ + 'python3', +- '-m', 'py_compile' ++ '-c', ++ script, + ] + list(filenames) + process = subprocess.Popen( + cmd, diff --git a/pkgs/applications/science/math/sage/patches/revert-269c1e1551285.patch b/pkgs/applications/science/math/sage/patches/revert-269c1e1551285.patch new file mode 100644 index 000000000000..b57e48b86dec --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/revert-269c1e1551285.patch @@ -0,0 +1,14 @@ +reverted: +--- b/src/sage/geometry/polyhedron/backend_cdd.py ++++ a/src/sage/geometry/polyhedron/backend_cdd.py +@@ -154,7 +154,9 @@ + ... [0.62, -1.38, 0.38],[0.144, -1.04, 0.04], + ... [0.1309090909, -1.0290909091, 0.04]] + sage: Polyhedron(point_list) ++ Traceback (most recent call last): ++ ... ++ ValueError: *Error: Numerical inconsistency is found. Use the GMP exact arithmetic. +- A 3-dimensional polyhedron in RDF^3 defined as the convex hull of 14 vertices + sage: Polyhedron(point_list, base_ring=QQ) + A 3-dimensional polyhedron in QQ^3 defined as the convex hull of 14 vertices + """ diff --git a/pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch b/pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch new file mode 100644 index 000000000000..42deef4eab0c --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch @@ -0,0 +1,31 @@ +From 7419e0246230594ebfd5e7a2fe6b80d67abfc98a Mon Sep 17 00:00:00 2001 +From: Jeroen Demeyer +Date: Tue, 20 Mar 2018 10:40:41 +0100 +Subject: Fix sphinxify doctests + +--- + sagenb/misc/sphinxify.py | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/sagenb/misc/sphinxify.py b/sagenb/misc/sphinxify.py +index 4f76d41..15623d9 100644 +--- a/sagenb/misc/sphinxify.py ++++ b/sagenb/misc/sphinxify.py +@@ -47,11 +47,11 @@ def sphinxify(docstring, format='html'): + + sage: from sage.misc.sphinxify import sphinxify + sage: sphinxify('A test') +- '...
    \n \n

    A test

    \n\n\n
    ' ++ '
    \n \n

    A test

    \n\n\n
    ' + sage: sphinxify('**Testing**\n`monospace`') +- '...
    Testing\n\n\n\n
    ' ++ '
    Testing\n\n\n\n
    ' + sage: sphinxify('`x=y`') +- '...
    \n \n

    x=y

    \n\n\n
    ' ++ '
    \n \n

    x=y

    \n\n\n
    ' + sage: sphinxify('`x=y`', format='text') + 'x=y\n' + sage: sphinxify(':math:`x=y`', format='text') +-- +cgit v1.0-1-gd88e + diff --git a/pkgs/applications/science/math/sage/patches/sphinx-1.7.patch b/pkgs/applications/science/math/sage/patches/sphinx-1.7.patch new file mode 100644 index 000000000000..c67b8942e28b --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/sphinx-1.7.patch @@ -0,0 +1,62 @@ +diff --git a/src/bin/sage b/src/bin/sage +index 397f30cbed..3fc473c343 100755 +--- a/src/bin/sage ++++ b/src/bin/sage +@@ -980,8 +980,11 @@ if [ "$1" = '-rsyncdist' -o "$1" = "--rsyncdist" ]; then + fi + + if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then ++ # Redirect stdin from /dev/null. This helps with running TeX which ++ # tends to ask interactive questions if something goes wrong. These ++ # cause the build to hang. If stdin is /dev/null, TeX just aborts. + shift +- exec sage-python23 -m "sage_setup.docbuild" "$@" ++ exec sage-python23 -m sage_setup.docbuild "$@" Introduction to the -adics ++
  • Introduction to the -adics
    • + """ + debug_inf(app, "???? Trying intersphinx for %s"%node['reftarget']) + builder = app.builder +diff --git a/src/sage/misc/sphinxify.py b/src/sage/misc/sphinxify.py +index 4f76d4113a..8f426b5989 100644 +--- a/src/sage/misc/sphinxify.py ++++ b/src/sage/misc/sphinxify.py +@@ -47,11 +47,11 @@ def sphinxify(docstring, format='html'): + + sage: from sage.misc.sphinxify import sphinxify + sage: sphinxify('A test') +- '...
    \n \n

    A test

    \n\n\n
    ' ++ '
    \n \n

    A test

    \n\n\n
    ' + sage: sphinxify('**Testing**\n`monospace`') +- '...
    Testing\n\n\n\n
    ' ++ '
    Testing\n\n \n

    x=y

    \n\n\n
    ' ++ '
    \n \n

    x=y

    \n\n\n
    ' + sage: sphinxify('`x=y`', format='text') + 'x=y\n' + sage: sphinxify(':math:`x=y`', format='text') +diff --git a/src/sage_setup/docbuild/sphinxbuild.py b/src/sage_setup/docbuild/sphinxbuild.py +index fda76a4174..d3413239dd 100644 +--- a/src/sage_setup/docbuild/sphinxbuild.py ++++ b/src/sage_setup/docbuild/sphinxbuild.py +@@ -207,7 +207,7 @@ def runsphinx(): + try: + sys.stdout = SageSphinxLogger(sys.stdout, os.path.basename(output_dir)) + sys.stderr = SageSphinxLogger(sys.stderr, os.path.basename(output_dir)) +- sphinx.cmdline.main(sys.argv) ++ sphinx.cmdline.main(sys.argv[1:]) + finally: + sys.stdout = saved_stdout + sys.stderr = saved_stderr diff --git a/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch b/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch new file mode 100644 index 000000000000..febab3702771 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch @@ -0,0 +1,31 @@ +diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py +index aa23c8405d..8a87de0591 100644 +--- a/src/sage/repl/ipython_kernel/install.py ++++ b/src/sage/repl/ipython_kernel/install.py +@@ -112,7 +112,7 @@ class SageKernelSpec(object): + EXAMPLES:: + + sage: from sage.repl.ipython_kernel.install import SageKernelSpec +- sage: spec = SageKernelSpec() ++ sage: spec = SageKernelSpec(prefix = tmp_dir()) + sage: spec.use_local_mathjax() + sage: mathjax = os.path.join(spec.nbextensions_dir, 'mathjax') + sage: os.path.isdir(mathjax) +@@ -129,7 +129,7 @@ class SageKernelSpec(object): + EXAMPLES:: + + sage: from sage.repl.ipython_kernel.install import SageKernelSpec +- sage: spec = SageKernelSpec() ++ sage: spec = SageKernelSpec(prefix = tmp_dir()) + sage: spec.use_local_jsmol() + sage: jsmol = os.path.join(spec.nbextensions_dir, 'jsmol') + sage: os.path.isdir(jsmol) +@@ -146,7 +146,7 @@ class SageKernelSpec(object): + EXAMPLES:: + + sage: from sage.repl.ipython_kernel.install import SageKernelSpec +- sage: spec = SageKernelSpec() ++ sage: spec = SageKernelSpec(prefix = tmp_dir()) + sage: spec.use_local_threejs() + sage: threejs = os.path.join(spec.nbextensions_dir, 'threejs') + sage: os.path.isdir(threejs) diff --git a/pkgs/applications/science/math/sage/patches/zn_poly_version.patch b/pkgs/applications/science/math/sage/patches/zn_poly_version.patch new file mode 100644 index 000000000000..92ea4303e477 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/zn_poly_version.patch @@ -0,0 +1,13 @@ +diff --git a/src/sage/misc/package.py b/src/sage/misc/package.py +index 7ff4f21675..1d72168833 100644 +--- a/src/sage/misc/package.py ++++ b/src/sage/misc/package.py +@@ -350,7 +350,7 @@ def package_versions(package_type, local=False): + sage: 'gap' in std + True + sage: std['zn_poly'] +- ('0.9.p11', '0.9.p11') ++ ('0.9', '0.9.p11') + """ + return {pkg['name']: (pkg['installed_version'], pkg['remote_version']) for pkg in list_packages(package_type, local=local).values()} + diff --git a/pkgs/applications/science/math/sage/pybrial.nix b/pkgs/applications/science/math/sage/pybrial.nix new file mode 100644 index 000000000000..f5cb39603c32 --- /dev/null +++ b/pkgs/applications/science/math/sage/pybrial.nix @@ -0,0 +1,29 @@ +{ stdenv +, fetchFromGitHub +, buildPythonPackage +}: +# This has a cyclic dependency with sage. I don't include sage in the +# buildInputs and let python figure it out at runtime. Because of this, +# I don't include the package in the main nipxkgs tree. It wouldn't be useful +# outside of sage anyways (as you could just directly depend on sage and use +# it). +buildPythonPackage rec { + pname = "pyBRiAl"; + version = "1.2.3"; + + # included with BRiAl source + src = fetchFromGitHub { + owner = "BRiAl"; + repo = "BRiAl"; + rev = "${version}"; + sha256 = "0qy4cwy7qrk4zg151cmws5cglaa866z461cnj9wdnalabs7v7qbg"; + }; + + sourceRoot = "source/sage-brial"; + + meta = with stdenv.lib; { + description = "python implementation of BRiAl"; + license = licenses.gpl2; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/pkgs/applications/science/math/sage/python-openid.nix b/pkgs/applications/science/math/sage/python-openid.nix new file mode 100644 index 000000000000..184eaf29bdd3 --- /dev/null +++ b/pkgs/applications/science/math/sage/python-openid.nix @@ -0,0 +1,42 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, isPy3k +, django +, nose +, twill +, pycrypto +}: + +buildPythonPackage rec { + pname = "python-openid"; + version = "2.2.5"; + + disabled = isPy3k; + + src = fetchPypi { + inherit pname version; + sha256 = "1vvhxlghjan01snfdc4k7ykd80vkyjgizwgg9bncnin8rqz1ricj"; + }; + + propagatedBuildInputs = [ + django + twill + pycrypto + ]; + + # Cannot access the djopenid example module. + # I don't know how to fix that (adding the examples dir to PYTHONPATH doesn't work) + doCheck = false; + checkInputs = [ nose ]; + checkPhase = '' + nosetests + ''; + + meta = with stdenv.lib; { + description = "OpenID library for Python"; + license = licenses.asl20; + maintainers = with maintainers; [ timokau ]; + homepage = https://github.com/openid/python-openid/; + }; +} diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix new file mode 100644 index 000000000000..317eb6e16c49 --- /dev/null +++ b/pkgs/applications/science/math/sage/sage-env.nix @@ -0,0 +1,162 @@ +{ stdenv +, lib +, writeTextFile +, python +, sage-src +, sagelib +, env-locations +, gfortran +, bash +, coreutils +, gnused +, gnugrep +, binutils +, pythonEnv +, python3 +, pkg-config +, pari +, gap-libgap-compatible +, libgap +, ecl +, maxima-ecl +, singular +, giac +, palp +, rWrapper +, gfan +, cddlib +, jmol +, tachyon +, glpk +, eclib +, sympow +, nauty +, sqlite +, ppl +, ecm +, lcalc +, rubiks +, flintqs +, openblas-cblas-pc +, flint +, gmp +, mpfr +, pynac +, zlib +, gsl +, ntl +}: + +let + runtimepath = (lib.makeBinPath ([ + "@sage-local@" + "@sage-local@/build" + pythonEnv + # empty python env to add python wrapper that clears PYTHONHOME (see + # wrapper.nix). This is necessary because sage will call the python3 binary + # (from python2 code). The python2 PYTHONHOME (again set in wrapper.nix) + # will then confuse python3, if it is not overwritten. + python3.buildEnv + gfortran # for inline fortran + stdenv.cc # for cython + bash + coreutils + gnused + gnugrep + binutils.bintools + pkg-config + pari + gap-libgap-compatible + libgap + ecl + maxima-ecl + singular + giac + palp + rWrapper + gfan + cddlib + jmol + tachyon + glpk + eclib + sympow + nauty + sqlite + ppl + ecm + lcalc + rubiks + flintqs + ] + )); +in +writeTextFile rec { + name = "sage-env"; + destination = "/${name}"; + text = '' + export PKG_CONFIG_PATH='${lib.concatStringsSep ":" (map (pkg: "${pkg}/lib/pkgconfig") [ + # This is only needed in the src/sage/misc/cython.py test and I'm not sure if there's really a use-case + # for it outside of the tests. However since singular and openblas are runtime dependencies anyways + # and openblas-cblas-pc is tiny, it doesn't really hurt to include. + singular + openblas-cblas-pc + ]) + }' + export SAGE_ROOT='${sage-src}' + export SAGE_LOCAL='@sage-local@' + export SAGE_SHARE='${sagelib}/share' + orig_path="$PATH" + export PATH='${runtimepath}' + + # set dependent vars, like JUPYTER_CONFIG_DIR + source "${sage-src}/src/bin/sage-env" + export PATH="${runtimepath}:$orig_path" # sage-env messes with PATH + + export SAGE_LOGS="$TMPDIR/sage-logs" + export SAGE_DOC="''${SAGE_DOC_OVERRIDE:-doc-placeholder}" + export SAGE_DOC_SRC="''${SAGE_DOC_SRC_OVERRIDE:-${sage-src}/src/doc}" + + # set locations of dependencies + . ${env-locations}/sage-env-locations + + # needed for cython + export CC='${stdenv.cc}/bin/${stdenv.cc.targetPrefix}cc' + # cython needs to find these libraries, otherwise will fail with `ld: cannot find -lflint` or similar + export LDFLAGS='${ + lib.concatStringsSep " " (map (pkg: "-L${pkg}/lib") [ + flint + libgap + glpk + gmp + mpfr + pari + pynac + zlib + eclib + gsl + ntl + jmol + sympow + ]) + }' + export CFLAGS='${ + lib.concatStringsSep " " (map (pkg: "-isystem ${pkg}/include") [ + singular + gmp.dev + glpk + flint + libgap + pynac + mpfr.dev + ]) + }' + + export SAGE_LIB='${sagelib}/${python.sitePackages}' + + export SAGE_EXTCODE='${sage-src}/src/ext' + + # for find_library + export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}:$DYLD_LIBRARY_PATH" + ''; +} 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..244a6ea72673 --- /dev/null +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -0,0 +1,205 @@ +{ 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 + # https://trac.sagemath.org/ticket/25546 + # https://trac.sagemath.org/ticket/25722 + (fetchpatch { + name = "install-jupyter-kernel-in-correct-prefix.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=72167b98e3f64326df6b2c78785df25539472fcc"; + sha256 = "0pscnjhm7r2yr2rxnv4kkkq626vwaja720lixa3m3w9rwlxll5a7"; + }) + ./patches/test-in-tmpdir.patch + + # 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; + }) + + # https://trac.sagemath.org/ticket/24927 rebased + ./patches/arb-2.13.0.patch + + # https://trac.sagemath.org/ticket/24838 rebased + ./patches/pynac-0.7.22.patch + ]; + + 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" + ''; +} diff --git a/pkgs/applications/science/math/sage/sage-with-env.nix b/pkgs/applications/science/math/sage/sage-with-env.nix new file mode 100644 index 000000000000..3d1ebe87c6b7 --- /dev/null +++ b/pkgs/applications/science/math/sage/sage-with-env.nix @@ -0,0 +1,129 @@ +{ stdenv +, lib +, makeWrapper +, sage-env +, sage-src +, sagelib +, sagedoc +, openblasCompat +, openblas-blas-pc +, openblas-cblas-pc +, openblas-lapack-pc +, pkg-config +, three +, singular +, libgap +, gap-libgap-compatible +, gcc +, giac +, maxima-ecl +, pari +, gmp +, gfan +, python2 +, flintqs +, eclib +, ntl +, ecm +, pynac +, pythonEnv +}: + +let + buildInputs = [ + pythonEnv # for patchShebangs + makeWrapper + pkg-config + openblasCompat # lots of segfaults with regular (64 bit) openblas + openblas-blas-pc + openblas-cblas-pc + openblas-lapack-pc + singular + three + pynac + giac + libgap + gap-libgap-compatible + pari + gmp + gfan + maxima-ecl + eclib + flintqs + ntl + ecm + ]; + + # remove python prefix, replace "-" in the name by "_", apply patch_names + # python2.7-some-pkg-1.0 -> some_pkg-1.0 + pkg_to_spkg_name = pkg: patch_names: let + parts = lib.splitString "-" pkg.name; + # remove python2.7- + stripped_parts = if (builtins.head parts) == python2.libPrefix then builtins.tail parts else parts; + version = lib.last stripped_parts; + orig_pkgname = lib.init stripped_parts; + pkgname = patch_names (lib.concatStringsSep "_" orig_pkgname); + in pkgname + "-" + version; + + + # return the names of all dependencies in the transitive closure + transitiveClosure = dep: + if isNull dep then + # propagatedBuildInputs might contain null + # (although that might be considered a programming error in the derivation) + [] + else + [ dep ] ++ ( + if builtins.hasAttr "propagatedBuildInputs" dep then + lib.unique (builtins.concatLists (map transitiveClosure dep.propagatedBuildInputs)) + else + [] + ); + + allInputs = lib.remove null (buildInputs ++ pythonEnv.extraLibs); + transitiveDeps = lib.unique (builtins.concatLists (map transitiveClosure allInputs )); + # fix differences between spkg and sage names + # (could patch sage instead, but this is more lightweight and also works for packages depending on sage) + patch_names = builtins.replaceStrings [ + "zope.interface" + "node_three" + ] [ + "zope_interface" + "threejs" + ]; + # spkg names (this_is_a_package-version) of all transitive deps + input_names = map (dep: pkg_to_spkg_name dep patch_names) transitiveDeps; +in +stdenv.mkDerivation rec { + version = sage-src.version; + name = "sage-with-env-${version}"; + + inherit buildInputs; + + src = sage-src; + + configurePhase = "#do nothing"; + + buildPhase = '' + mkdir installed + for pkg in ${lib.concatStringsSep " " input_names}; do + touch "installed/$pkg" + done + ''; + + installPhase = '' + mkdir -p "$out/var/lib/sage" + cp -r installed $out/var/lib/sage + + mkdir -p "$out/etc" + # sage tests will try to create this file if it doesn't exist + touch "$out/etc/sage-started.txt" + + mkdir -p "$out/build" + cp -r src/bin "$out/bin" + cp -r build/bin "$out/build/bin" + cp -f '${sage-env}/sage-env' "$out/bin/sage-env" + substituteInPlace "$out/bin/sage-env" \ + --subst-var-by sage-local "$out" + ''; +} diff --git a/pkgs/applications/science/math/sage/sage-wrapper.nix b/pkgs/applications/science/math/sage/sage-wrapper.nix new file mode 100644 index 000000000000..06b667f426fa --- /dev/null +++ b/pkgs/applications/science/math/sage/sage-wrapper.nix @@ -0,0 +1,41 @@ +{ stdenv +, makeWrapper +, sage +, sage-src +, sagedoc +, withDoc +}: + +stdenv.mkDerivation rec { + version = sage.version; + name = "sage-wrapper-${version}"; + + buildInputs = [ + makeWrapper + ]; + + unpackPhase = "#do nothing"; + configurePhase = "#do nothing"; + buildPhase = "#do nothing"; + + installPhase = '' + mkdir -p "$out/bin" + makeWrapper "${sage}/bin/sage" "$out/bin/sage" \ + --set SAGE_DOC_SRC_OVERRIDE "${sage-src}/src/doc" ${ + stdenv.lib.optionalString withDoc "--set SAGE_DOC_OVERRIDE ${sagedoc}/share/doc/sage" + } + ''; + + doInstallCheck = withDoc; + installCheckPhase = '' + export HOME="$TMPDIR/sage-home" + mkdir -p "$HOME" + "$out/bin/sage" -c 'browse_sage_doc._open("reference", testing=True)' + ''; + + meta = with stdenv.lib; { + description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"; + license = licenses.gpl2; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/pkgs/applications/science/math/sage/sage.nix b/pkgs/applications/science/math/sage/sage.nix new file mode 100644 index 000000000000..b1e5d7278b0f --- /dev/null +++ b/pkgs/applications/science/math/sage/sage.nix @@ -0,0 +1,32 @@ +{ stdenv +, sage-with-env +, makeWrapper +}: + +stdenv.mkDerivation rec { + version = sage-with-env.version; + name = "sage-${version}"; + + buildInputs = [ + makeWrapper + ]; + + unpackPhase = "#do nothing"; + configurePhase = "#do nothing"; + buildPhase = "#do nothing"; + + installPhase = '' + mkdir -p "$out/bin" + # Like a symlink, but make sure that $0 points to the original. + makeWrapper "${sage-with-env}/bin/sage" "$out/bin/sage" + ''; + + doInstallCheck = true; + installCheckPhase = '' + export HOME="$TMPDIR/sage-home" + mkdir -p "$HOME" + + # "--long" tests are in the order of 1h, without "--long" its 1/2h + "$out/bin/sage" -t --nthreads "$NIX_BUILD_CORES" --optional=sage --long --all + ''; +} diff --git a/pkgs/applications/science/math/sage/sagedoc.nix b/pkgs/applications/science/math/sage/sagedoc.nix new file mode 100644 index 000000000000..7b280e9e0280 --- /dev/null +++ b/pkgs/applications/science/math/sage/sagedoc.nix @@ -0,0 +1,97 @@ +{ pkgs +, stdenv +, sage-src +, env-locations +, sage-with-env +, sagelib +, python2 +, psutil +, future +, sphinx +, sagenb +, maxima-ecl +, networkx +, scipy +, sympy +, matplotlib +, pillow +, ipykernel +, jupyter_client +, tachyon +, jmol +, ipywidgets +, typing +, cddlib +, pybrial +}: + +stdenv.mkDerivation rec { + version = sage-src.version; + name = "sagedoc-${version}"; + + + # Building the documentation has many dependencies, because all documented + # modules are imported and because matplotlib is used to produce plots. + buildInputs = [ + sagelib + python2 + psutil + future + sphinx + sagenb + maxima-ecl + networkx + scipy + sympy + matplotlib + pillow + ipykernel + jupyter_client + tachyon + jmol + ipywidgets + typing + cddlib + pybrial + ]; + + unpackPhase = '' + export SAGE_DOC_OVERRIDE="$PWD/share/doc/sage" + export SAGE_DOC_SRC_OVERRIDE="$PWD/docsrc" + + cp -r "${sage-src}/src/doc" "$SAGE_DOC_SRC_OVERRIDE" + chmod -R 755 "$SAGE_DOC_SRC_OVERRIDE" + ''; + + buildPhase = '' + export SAGE_NUM_THREADS="$NIX_BUILD_CORES" + export HOME="$TMPDIR/sage_home" + mkdir -p "$HOME" + + ${sage-with-env}/bin/sage -python -m sage_setup.docbuild \ + --mathjax \ + --no-pdf-links \ + all html + ''; + + installPhase = '' + cd "$SAGE_DOC_OVERRIDE" + + mkdir -p "$out/share/doc/sage" + cp -r html "$out"/share/doc/sage + + # Replace duplicated files by symlinks (Gentoo) + cd "$out"/share/doc/sage + mv html/en/_static{,.tmp} + for _dir in `find -name _static` ; do + rm -r $_dir + ln -s /share/doc/sage/html/en/_static $_dir + done + mv html/en/_static{.tmp,} + ''; + + doCheck = true; + checkPhase = '' + ${sage-with-env}/bin/sage -t --optional=dochtml --all + ''; +} diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix new file mode 100644 index 000000000000..a053d997bf9a --- /dev/null +++ b/pkgs/applications/science/math/sage/sagelib.nix @@ -0,0 +1,139 @@ +{ stdenv +, sage-src +, perl +, buildPythonPackage +, arb +, openblasCompat +, openblas-blas-pc +, openblas-cblas-pc +, openblas-lapack-pc +, brial +, cliquer +, cypari2 +, cysignals +, cython +, ecl +, eclib +, ecm +, flint +, gd +, givaro +, glpk +, gsl +, iml +, jinja2 +, lcalc +, lrcalc +, libgap +, linbox +, m4ri +, m4rie +, libmpc +, mpfi +, ntl +, numpy +, pari +, pkgconfig +, planarity +, ppl +, pynac +, python +, ratpoints +, readline +, rankwidth +, symmetrica +, zn_poly +, fflas-ffpack +, boost +, singular +, pip +, jupyter_core +}: + +buildPythonPackage rec { + format = "other"; + version = sage-src.version; + pname = "sagelib"; + + src = sage-src; + + nativeBuildInputs = [ + iml + perl + openblas-blas-pc + openblas-cblas-pc + openblas-lapack-pc + jupyter_core + ]; + + buildInputs = [ + gd + readline + ]; + + propagatedBuildInputs = [ + cypari2 + jinja2 + numpy + pkgconfig + boost + arb + brial + cliquer + ecl + eclib + ecm + fflas-ffpack + flint + givaro + glpk + gsl + lcalc + libgap + libmpc + linbox + lrcalc + m4ri + m4rie + mpfi + ntl + openblasCompat + pari + planarity + ppl + pynac + rankwidth + ratpoints + singular + symmetrica + zn_poly + pip + cython + cysignals + ]; + + buildPhase = '' + export SAGE_ROOT="$PWD" + export SAGE_LOCAL="$SAGE_ROOT" + export SAGE_SHARE="$SAGE_LOCAL/share" + export JUPYTER_PATH="$SAGE_LOCAL/jupyter" + + export PATH="$SAGE_ROOT/build/bin:$SAGE_ROOT/src/bin:$PATH" + + export SAGE_NUM_THREADS="$NIX_BUILD_CORES" + + mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython" + mkdir -p "var/lib/sage/installed" + + cd src + source bin/sage-dist-helpers + + ${python.interpreter} -u setup.py --no-user-cfg build + ''; + + installPhase = '' + ${python.interpreter} -u setup.py --no-user-cfg install --prefix=$out + + rm -r "$out/${python.sitePackages}/sage/cython_debug" + ''; +} diff --git a/pkgs/applications/science/math/sage/sagenb.nix b/pkgs/applications/science/math/sage/sagenb.nix new file mode 100644 index 000000000000..5ab387ebc5e1 --- /dev/null +++ b/pkgs/applications/science/math/sage/sagenb.nix @@ -0,0 +1,49 @@ +# Has a cyclic dependency with sage (not expressed here) and is not useful outside of sage +{ stdenv +, fetchpatch +, python +, buildPythonPackage +, fetchFromGitHub +, mathjax +, twisted +, flask +, flask-oldsessions +, flask-openid +, flask-autoindex +, flask-babel +}: + +buildPythonPackage rec { + pname = "sagenb"; + version = "2018-06-26"; # not 1.0.1 because of new flask syntax + + src = fetchFromGitHub { + owner = "sagemath"; + repo = "sagenb"; + rev = "b360a0172e15501fb0163d02dce713a561fee2af"; + sha256 = "12anydw0v9w23rbc0a94bqmjhjdir9h820c5zdhipw9ccdcc2jlf"; + }; + + propagatedBuildInputs = [ + twisted + flask + flask-oldsessions + flask-openid + flask-autoindex + flask-babel + ]; + + # tests depend on sage + doCheck = false; + + meta = with stdenv.lib; { + description = "Sage Notebook"; + license = licenses.gpl3Plus; + maintainers = with maintainers; [ timokau ]; + }; + + # let sagenb use mathjax + postInstall = '' + ln -s ${mathjax}/lib/node_modules/mathjax "$out/${python.sitePackages}/mathjax" + ''; +} diff --git a/pkgs/applications/science/math/sage/shebangs.patch b/pkgs/applications/science/math/sage/shebangs.patch deleted file mode 100644 index 96ed5a4bc6c3..000000000000 --- a/pkgs/applications/science/math/sage/shebangs.patch +++ /dev/null @@ -1,36 +0,0 @@ -diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg -index 83e61a7e0d..942ba206c7 100755 ---- a/build/bin/sage-spkg -+++ b/build/bin/sage-spkg -@@ -648,8 +648,12 @@ if ! sage-apply-patches; then - error_msg "Error applying patches" - exit 1 - fi -+ -+@bash@/bin/bash @patchSageShebangs@ . -+ - cd .. - -+ - ################################################################## - # The package has been extracted, prepare for installation - ################################################################## -@@ -671,7 +675,7 @@ write_script_wrapper() { - local tmpscript="$(dirname "$script")/.tmp-${script##*/}" - - cat > "$tmpscript" <<__EOF__ --#!/usr/bin/env bash -+#! @bash@/bin/bash - - export SAGE_ROOT="$SAGE_ROOT" - export SAGE_SRC="$SAGE_SRC" -@@ -833,6 +837,9 @@ if [ "$UNAME" = "CYGWIN" ]; then - sage-rebase.sh "$SAGE_LOCAL" 2>/dev/null - fi - -+@bash@/bin/bash @patchSageShebangs@ . -+@bash@/bin/bash @patchSageShebangs@ "$out/bin" -+ - echo "Successfully installed $PKG_NAME" - - if [ "$SAGE_CHECK" = "yes" ]; then diff --git a/pkgs/applications/science/math/sage/spkg-giac.patch b/pkgs/applications/science/math/sage/spkg-giac.patch deleted file mode 100644 index c79d4422133d..000000000000 --- a/pkgs/applications/science/math/sage/spkg-giac.patch +++ /dev/null @@ -1,20 +0,0 @@ -diff --git a/build/pkgs/giac/spkg-install b/build/pkgs/giac/spkg-install -index bdd8df6cb8..3fd7a3ef8a 100644 ---- a/build/pkgs/giac/spkg-install -+++ b/build/pkgs/giac/spkg-install -@@ -2,6 +2,15 @@ - ## Giac - ########################################### - -+# Fix hardcoded paths, while making sure to only update timestamps of actually -+# changed files (otherwise confuses make) -+grep -rlF '/bin/cp' . | while read file -+do -+ sed -e 's@/bin/cp@cp@g' -i "$file" -+done -+ -+# Fix input parser syntax -+sed -e 's@yylex (&yylval)@yylex (\&yyval, scanner)@gp' -i 'src/src/input_parser.cc' - - if [ "$SAGE_LOCAL" = "" ]; then - echo "SAGE_LOCAL undefined ... exiting"; diff --git a/pkgs/applications/science/math/sage/spkg-git.patch b/pkgs/applications/science/math/sage/spkg-git.patch deleted file mode 100644 index 74f552dd3c36..000000000000 --- a/pkgs/applications/science/math/sage/spkg-git.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/build/pkgs/git/spkg-install b/build/pkgs/git/spkg-install -index 87874de3d8..b0906245fa 100644 ---- a/build/pkgs/git/spkg-install -+++ b/build/pkgs/git/spkg-install -@@ -33,6 +33,13 @@ fi - - cd src - -+# Fix hardcoded paths, while making sure to only update timestamps of actually -+# changed files (otherwise confuses make) -+grep -rlF '/usr/bin/perl' . | while read file -+do -+ sed -e 's@/usr/bin/perl@perl@g' -i "$file" -+done -+ - # We don't want to think about Fink or Macports - export NO_FINK=1 - export NO_DARWIN_PORTS=1 diff --git a/pkgs/applications/science/math/sage/spkg-python.patch b/pkgs/applications/science/math/sage/spkg-python.patch deleted file mode 100644 index e39981b6552a..000000000000 --- a/pkgs/applications/science/math/sage/spkg-python.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/build/pkgs/python3/spkg-build b/build/pkgs/python3/spkg-build -index 56db087ae5..b450703c5f 100644 ---- a/build/pkgs/python3/spkg-build -+++ b/build/pkgs/python3/spkg-build -@@ -27,6 +27,8 @@ fi - export EXTRA_CFLAGS="`testcflags.sh -Wno-unused` $CFLAGS" - unset CFLAGS - -+export LDFLAGS="$LDFLAGS -lcrypt" -+ - if [ "$UNAME" = Darwin ]; then - PYTHON_CONFIGURE="--disable-toolbox-glue $PYTHON_CONFIGURE" - diff --git a/pkgs/applications/science/math/sage/spkg-singular.patch b/pkgs/applications/science/math/sage/spkg-singular.patch deleted file mode 100644 index 606ffcd3ad4e..000000000000 --- a/pkgs/applications/science/math/sage/spkg-singular.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/build/pkgs/singular/spkg-install b/build/pkgs/singular/spkg-install -index 8caafb1699..3c34e6608a 100644 ---- a/build/pkgs/singular/spkg-install -+++ b/build/pkgs/singular/spkg-install -@@ -2,6 +2,13 @@ - ## Singular - ########################################### - -+# Fix hardcoded paths, while making sure to only update timestamps of actually -+# changed files (otherwise confuses make) -+grep -rlF '/bin/rm' . | while read file -+do -+ sed -e 's@/bin/rm@rm@g' -i "$file" -+done -+ - if [ -z "$SAGE_LOCAL" ]; then - echo >&2 "Error: SAGE_LOCAL undefined -- exiting..." - echo >&2 "Maybe run 'sage -sh'?" diff --git a/pkgs/applications/science/math/symmetrica/default.nix b/pkgs/applications/science/math/symmetrica/default.nix index a7212299aa63..6123fd7306d9 100644 --- a/pkgs/applications/science/math/symmetrica/default.nix +++ b/pkgs/applications/science/math/symmetrica/default.nix @@ -1,14 +1,15 @@ -{stdenv, fetchurl}: +{ stdenv +, fetchurl +, fetchpatch +}: stdenv.mkDerivation rec { name = "symmetrica-${version}"; version = "2.0"; - # or fetchFromGitHub(owner,repo,rev) or fetchgit(rev) src = fetchurl { url = "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/SYM2_0_tar.gz"; sha256 = "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"; name = "symmetrica-2.0.tar.gz"; }; - buildInputs = []; sourceRoot = "."; installPhase = '' mkdir -p "$out"/{lib,share/doc/symmetrica,include/symmetrica} @@ -18,6 +19,22 @@ stdenv.mkDerivation rec { cp *.h "$out/include/symmetrica" cp README *.doc "$out/share/doc/symmetrica" ''; + patches = [ + # don't show banner ("SYMMETRICA VERSION X - STARTING) + # it doesn't contain very much helpful information and a banner is not ideal for a library + (fetchpatch { + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/de.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "0df0vqixcfpzny6dkhyj87h8aznz3xn3zfwwlj8pd10bpb90k6gb"; + }) + + # use int32_t and uint32_t for type INT + # see https://trac.sagemath.org/ticket/13413 + (fetchpatch { + name = "fix_64bit_integer_overflow.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/int32.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "0p33c85ck4kd453z687ni4bdcqr1pqx2756j7aq11bf63vjz4cyz"; + }) + ]; meta = { inherit version; description = ''A collection of routines for representation theory and combinatorics''; diff --git a/pkgs/build-support/fetchurl/mirrors.nix b/pkgs/build-support/fetchurl/mirrors.nix index 2d1773531532..d5f29e3daf1b 100644 --- a/pkgs/build-support/fetchurl/mirrors.nix +++ b/pkgs/build-support/fetchurl/mirrors.nix @@ -319,51 +319,48 @@ rec { ]; # Sage mirrors (http://www.sagemath.org/mirrors.html) - sagemath = [ + sageupstream = [ # Africa - http://sagemath.polytechnic.edu.na/src/ - ftp://ftp.sun.ac.za/pub/mirrors/www.sagemath.org/src/ - http://sagemath.mirror.ac.za/src/ - https://ftp.leg.uct.ac.za/pub/packages/sage/src/ - http://mirror.ufs.ac.za/sagemath/src/ + http://sagemath.polytechnic.edu.na/spkg/upstream/ + ftp://ftp.sun.ac.za/pub/mirrors/www.sagemath.org/spkg/upstream/ + http://sagemath.mirror.ac.za/spkg/upstream/ + https://ftp.leg.uct.ac.za/pub/packages/sage/spkg/upstream/ + http://mirror.ufs.ac.za/sagemath/spkg/upstream/ # America, North - http://mirrors-usa.go-parts.com/sage/sagemath/src/ - http://mirrors.mit.edu/sage/src/ - http://www.cecm.sfu.ca/sage/src/ - http://files.sagemath.org/src/ - http://mirror.clibre.uqam.ca/sage/src/ - https://mirrors.xmission.com/sage/src/ + http://mirrors-usa.go-parts.com/sage/sagemath/spkg/upstream/ + http://mirrors.mit.edu/sage/spkg/upstream/ + http://www.cecm.sfu.ca/sage/spkg/upstream/ + http://files.sagemath.org/spkg/upstream/ + http://mirror.clibre.uqam.ca/sage/spkg/upstream/ + https://mirrors.xmission.com/sage/spkg/upstream/ # America, South - http://sagemath.c3sl.ufpr.br/src/ - http://linorg.usp.br/sage/ + http://sagemath.c3sl.ufpr.br/spkg/upstream/ + http://linorg.usp.br/sage/spkg/upstream # Asia - http://sage.asis.io/src/ - http://mirror.hust.edu.cn/sagemath/src/ - https://ftp.iitm.ac.in/sage/src/ - http://ftp.kaist.ac.kr/sage/src/ - http://ftp.riken.jp/sagemath/src/ - https://mirrors.tuna.tsinghua.edu.cn/sagemath/src/ - https://mirrors.ustc.edu.cn/sagemath/src/ - http://ftp.tsukuba.wide.ad.jp/software/sage/src/ - http://ftp.yz.yamagata-u.ac.jp/pub/math/sage/src/ - https://mirror.yandex.ru/mirrors/sage.math.washington.edu/src/ + http://sage.asis.io/spkg/upstream/ + http://mirror.hust.edu.cn/sagemath/spkg/upstream/ + https://ftp.iitm.ac.in/sage/spkg/upstream/ + http://ftp.kaist.ac.kr/sage/spkg/upstream/ + http://ftp.riken.jp/sagemath/spkg/upstream/ + https://mirrors.tuna.tsinghua.edu.cn/sagemath/spkg/upstream/ + https://mirrors.ustc.edu.cn/sagemath/spkg/upstream/ + http://ftp.tsukuba.wide.ad.jp/software/sage/spkg/upstream/ + http://ftp.yz.yamagata-u.ac.jp/pub/math/sage/spkg/upstream/ + https://mirror.yandex.ru/mirrors/sage.math.washington.edu/spkg/upstream/ # Australia - http://echidna.maths.usyd.edu.au/sage/src/ + http://echidna.maths.usyd.edu.au/sage/spkg/upstream/ # Europe - http://sage.mirror.garr.it/mirrors/sage/src/ - http://sunsite.rediris.es/mirror/sagemath/src/ - http://mirror.switch.ch/mirror/sagemath/src/ - http://mirrors.fe.up.pt/pub/sage/src/ - http://www-ftp.lip6.fr/pub/math/sagemath/src/ - http://ftp.ntua.gr/pub/sagemath/src/ - - # Old versions - http://sagemath.org/src-old/ + http://sage.mirror.garr.it/mirrors/sage/spkg/upstream/ + http://sunsite.rediris.es/mirror/sagemath/spkg/upstream/ + http://mirror.switch.ch/mirror/sagemath/spkg/upstream/ + http://mirrors.fe.up.pt/pub/sage/spkg/upstream/ + http://www-ftp.lip6.fr/pub/math/sagemath/spkg/upstream/ + http://ftp.ntua.gr/pub/sagemath/spkg/upstream/ ]; # MySQL mirrors diff --git a/pkgs/data/misc/combinatorial_designs/default.nix b/pkgs/data/misc/combinatorial_designs/default.nix new file mode 100644 index 000000000000..18331b5ada9d --- /dev/null +++ b/pkgs/data/misc/combinatorial_designs/default.nix @@ -0,0 +1,31 @@ +{ stdenv +, fetchurl +}: + +stdenv.mkDerivation rec { + name = "combinatorial_designs-${version}"; + version = "20140630"; + + src = fetchurl { + url = "mirror://sageupstream/combinatorial_designs/combinatorial_designs-${version}.tar.bz2"; + sha256 = "0bj8ngiq59hipa6izi6g5ph5akmy4cbk0vlsb0wa67f7grnnqj69"; + }; + + installPhase = '' + mkdir -p "$out/share/combinatorial_designs" + mv * "$out/share/combinatorial_designs" + ''; + + meta = with stdenv.lib; { + description = "Data for Combinatorial Designs"; + longDescription = '' + Current content: + + - The table of MOLS (10 000 integers) from the Handbook of Combinatorial + Designs, 2ed. + ''; + license = licenses.publicDomain; + platforms = platforms.all; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/pkgs/data/misc/conway_polynomials/default.nix b/pkgs/data/misc/conway_polynomials/default.nix new file mode 100644 index 000000000000..fec422b33acf --- /dev/null +++ b/pkgs/data/misc/conway_polynomials/default.nix @@ -0,0 +1,43 @@ +{ stdenv +, fetchurl +, python +}: + +stdenv.mkDerivation rec { + name = "conway_polynomials-${version}"; + version = "0.5"; + + pythonEnv = python.withPackages (ps: with ps; [ six ]); + + src = fetchurl { + url = "mirror://sageupstream/conway_polynomials/conway_polynomials-${version}.tar.bz2"; + sha256 = "05zb1ly9x2bbscqv0jgc45g48xx77mfs7qdbqhn4ihmihn57iwnq"; + }; + + # Script that creates the "database" (nested python array) and pickles it + spkg-install = fetchurl { + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/conway_polynomials/spkg-install.py?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "0m12nfb37j3bn4bp06ddgnyp2d6z0hg5f83pbbjszxw7vxs33a82"; + }; + + installPhase = '' + # directory layout as spkg-install.py expects + dir="$PWD" + cd .. + ln -s "$dir" "src" + + # environment spkg-install.py expects + mkdir -p "$out/share" + export SAGE_SHARE="$out/share" + export PYTHONPATH=$PWD + + ${pythonEnv.interpreter} ${spkg-install} + ''; + + meta = with stdenv.lib; { + description = "Contains a small database of Conway polynomials."; + license = licenses.gpl2; + platforms = platforms.all; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/pkgs/data/misc/elliptic_curves/default.nix b/pkgs/data/misc/elliptic_curves/default.nix new file mode 100644 index 000000000000..528486328c68 --- /dev/null +++ b/pkgs/data/misc/elliptic_curves/default.nix @@ -0,0 +1,51 @@ +{ stdenv +, fetchurl +, python +}: + +stdenv.mkDerivation rec { + pname = "elliptic_curves"; + version = "0.8"; + name = "${pname}-${version}"; + + src = fetchurl { + url = "mirror://sageupstream/${pname}/${pname}-${version}.tar.bz2"; + sha256 = "0pzaym44x88dn8rydiwqgm73yghzlgf7gqvd7qqsrsdl2vyp091w"; + }; + + + # Script that creates the sqlite database from the allcurves textfile + spkg-install = fetchurl { + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/${pname}/spkg-install.py?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "116g684i6mvs11fvb6fzfsr4fn903axn31vigdyb8bgpf8l4hvc5"; + }; + + installPhase = '' + # directory layout as spkg-install.py expects + dir="$PWD" + cd .. + ln -s "$dir" "src" + + # environment spkg-install.py expects + mkdir -p "$out/share" + export SAGE_SHARE="$out/share" + export PYTHONPATH=$PWD + + ${python.interpreter} ${spkg-install} + ''; + + meta = with stdenv.lib; { + description = "Databases of elliptic curves"; + longDescription = '' + Includes two databases: + + * A small subset of the data in John Cremona's database of elliptic curves up + to conductor 10000. See http://www.warwick.ac.uk/~masgaj/ftp/data/ or + http://sage.math.washington.edu/cremona/INDEX.html + * William Stein's database of interesting curves + ''; + license = licenses.gpl2; + platforms = platforms.all; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/pkgs/data/misc/graphs/default.nix b/pkgs/data/misc/graphs/default.nix new file mode 100644 index 000000000000..aea5feef46c7 --- /dev/null +++ b/pkgs/data/misc/graphs/default.nix @@ -0,0 +1,26 @@ +{ stdenv +, fetchurl +}: + +stdenv.mkDerivation rec { + pname = "graphs"; + version = "20161026"; + name = "${pname}-${version}"; + + src = fetchurl { + url = "mirror://sageupstream/${pname}/${pname}-${version}.tar.bz2"; + sha256 = "0a2b5lly9nifphvknz88rrhfbbc8vqnlqcv19zdpfq8h8nnyjbb2"; + }; + + installPhase = '' + mkdir -p "$out/share/graphs" + cp * "$out/share/graphs/" + ''; + + meta = with stdenv.lib; { + description = "A database of graphs"; + license = licenses.gpl2; + platforms = platforms.all; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/pkgs/data/misc/pari-galdata/default.nix b/pkgs/data/misc/pari-galdata/default.nix new file mode 100644 index 000000000000..222fd2f88707 --- /dev/null +++ b/pkgs/data/misc/pari-galdata/default.nix @@ -0,0 +1,26 @@ +{ stdenv +, fetchurl +}: + +stdenv.mkDerivation rec { + version = "20080411"; + name = "pari-galdata-${version}"; + + src = fetchurl { + url = "http://pari.math.u-bordeaux.fr/pub/pari/packages/galdata.tgz"; + sha256 = "1pch6bk76f1i6cwwgm7hhxi5h71m52lqayp4mnyj0jmjk406bhdp"; + }; + + installPhase = '' + mkdir -p "$out/share/pari" + cp -R * "$out/share/pari/" + ''; + + meta = with stdenv.lib; { + description = "PARI database needed to compute Galois group in degrees 8 through 11"; + homepage = http://pari.math.u-bordeaux.fr/; + license = licenses.gpl2Plus; + platforms = platforms.all; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/pkgs/data/misc/pari-seadata-small/default.nix b/pkgs/data/misc/pari-seadata-small/default.nix new file mode 100644 index 000000000000..967122c1bd4d --- /dev/null +++ b/pkgs/data/misc/pari-seadata-small/default.nix @@ -0,0 +1,26 @@ +{ stdenv +, fetchurl +}: + +stdenv.mkDerivation rec { + version = "20090618"; + name = "pari-seadata-small-${version}"; + + src = fetchurl { + url = "http://pari.math.u-bordeaux.fr/pub/pari/packages/seadata-small.tgz"; + sha256 = "13qafribxwkz8h3haa0cng7arz0kh7398br4y7vqs9ib8w9yjnxz"; + }; + + installPhase = '' + mkdir -p "$out/share/pari" + cp -R * "$out/share/pari/" + ''; + + meta = with stdenv.lib; { + description = "PARI database needed by ellap for large primes"; + homepage = http://pari.math.u-bordeaux.fr/; + license = licenses.gpl2Plus; + platforms = platforms.all; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/pkgs/data/misc/polytopes_db/default.nix b/pkgs/data/misc/polytopes_db/default.nix new file mode 100644 index 000000000000..85f2cff09db2 --- /dev/null +++ b/pkgs/data/misc/polytopes_db/default.nix @@ -0,0 +1,26 @@ +{ stdenv +, fetchurl +}: + +stdenv.mkDerivation rec { + pname = "polytopes_db"; + version = "20170220"; + name = "${pname}-${version}"; + + src = fetchurl { + url = "mirror://sageupstream/${pname}/${pname}-${version}.tar.bz2"; + sha256 = "1q0cd811ilhax4dsj9y5p7z8prlalqr7k9mzq178c03frbgqny6b"; + }; + + installPhase = '' + mkdir -p "$out/share/reflexive_polytopes" + cp -R * "$out/share/reflexive_polytopes/" + ''; + + meta = with stdenv.lib; { + description = "Reflexive polytopes database"; + license = licenses.gpl2; + platforms = platforms.all; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/pkgs/development/compilers/ecl/16.1.2.nix b/pkgs/development/compilers/ecl/16.1.2.nix index 291b0ed013d6..c27f2a226705 100644 --- a/pkgs/development/compilers/ecl/16.1.2.nix +++ b/pkgs/development/compilers/ecl/16.1.2.nix @@ -53,6 +53,14 @@ stdenv.mkDerivation { url = "https://gitlab.com/embeddable-common-lisp/ecl/commit/caba1989f40ef917e7486f41b9cd5c7e3c5c2d79.patch"; sha256 = "07vw91psbc9gdn8grql46ra8lq3bgkzg5v480chnbryna4sv6lbb"; }) + (fetchpatch { + # Fix getcwd with long pathnames + # Rebased version of + # https://gitlab.com/embeddable-common-lisp/ecl/commit/ac5f011f57a85a38627af154bc3ee7580e7fecd4.patch + name = "getcwd.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/ecl/patches/16.1.2-getcwd.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "1fbi8gn7rv8nqff5mpaijsrch3k3z7qc5cn4h1vl8qrr8xwqlqhb"; + }) ]; hardeningDisable = [ "format" ]; diff --git a/pkgs/development/libraries/arb/default.nix b/pkgs/development/libraries/arb/default.nix index a59641e99d39..ea70e6454536 100644 --- a/pkgs/development/libraries/arb/default.nix +++ b/pkgs/development/libraries/arb/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchFromGitHub, mpir, gmp, mpfr, flint}: +{stdenv, fetchFromGitHub, fetchpatch, mpir, gmp, mpfr, flint}: stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "arb"; @@ -17,6 +17,14 @@ stdenv.mkDerivation rec { "--with-flint=${flint}" ]; doCheck = true; + patches = [ + # https://github.com/fredrik-johansson/arb/pull/210, included in next release + (fetchpatch { + url = "https://patch-diff.githubusercontent.com/raw/fredrik-johansson/arb/pull/210.patch"; + name = "return-exact-zero-where-possible.patch"; + sha256 = "01j9npnpmwh4dla9i05qdn606hy34gy9bz7c9bbsqm7az3n7pxjg"; + }) + ]; meta = { inherit version; description = ''A library for arbitrary-precision interval arithmetic''; diff --git a/pkgs/development/libraries/libgap/default.nix b/pkgs/development/libraries/libgap/default.nix index dec9676d5729..42e812ec1f53 100644 --- a/pkgs/development/libraries/libgap/default.nix +++ b/pkgs/development/libraries/libgap/default.nix @@ -1,10 +1,17 @@ -{stdenv, fetchurl, gmp}: +{ stdenv +, fetchurl +, gmp +}: +# will probably be obsolte (or at leat built from the upstream gap sources) soon (gap 4.9?). See +# - https://github.com/gap-system/gap/projects/5#card-6239828 +# - https://github.com/markuspf/gap/issues/2 +# - https://trac.sagemath.org/ticket/22626 stdenv.mkDerivation rec { name = "libgap-${version}"; + # Has to be the same version as "gap" version = "4.8.6"; - # or fetchFromGitHub(owner,repo,rev) or fetchgit(rev) src = fetchurl { - url = "http://mirrors.mit.edu/sage/spkg/upstream/libgap/libgap-${version}.tar.gz"; + url = "mirror://sageupstream/libgap/libgap-${version}.tar.gz"; sha256 = "1h5fx5a55857w583ql7ly2jl49qyx9mvs7j5abys00ra9gzrpn5v"; }; buildInputs = [gmp]; diff --git a/pkgs/development/libraries/linbox/default.nix b/pkgs/development/libraries/linbox/default.nix index 0f5442bd63b6..c4ff0e892a82 100644 --- a/pkgs/development/libraries/linbox/default.nix +++ b/pkgs/development/libraries/linbox/default.nix @@ -5,7 +5,6 @@ , givaro , pkgconfig , openblas -, liblapack , fflas-ffpack , gmpxx , optimize ? false # impure @@ -30,7 +29,6 @@ stdenv.mkDerivation rec { buildInputs = [ givaro - (liblapack.override {shared = true;}) openblas gmpxx fflas-ffpack @@ -38,7 +36,6 @@ stdenv.mkDerivation rec { configureFlags = [ "--with-blas-libs=-lopenblas" - "--with-lapack-libs=-llapack" "--disable-optimization" ] ++ stdenv.lib.optionals (!optimize) [ # disable SIMD instructions (which are enabled *when available* by default) diff --git a/pkgs/development/libraries/science/math/lcalc/default.nix b/pkgs/development/libraries/science/math/lcalc/default.nix index 90393cff001c..6bbd43b0c848 100644 --- a/pkgs/development/libraries/science/math/lcalc/default.nix +++ b/pkgs/development/libraries/science/math/lcalc/default.nix @@ -12,7 +12,7 @@ stdenv.mkDerivation rec { src = fetchurl { # original at http://oto.math.uwaterloo.ca/~mrubinst/L_function_public/CODE/L-${version}.tar.gz, no longer available # "newer" version at google code https://code.google.com/archive/p/l-calc/source/default/source - url = "http://mirrors.mit.edu/sage/spkg/upstream/lcalc/lcalc-${version}.tar.bz2"; + url = "mirror://sageupstream/lcalc/lcalc-${version}.tar.bz2"; sha256 = "1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43"; }; diff --git a/pkgs/development/libraries/science/math/openblas/default.nix b/pkgs/development/libraries/science/math/openblas/default.nix index bd095a11f088..91162ba5465a 100644 --- a/pkgs/development/libraries/science/math/openblas/default.nix +++ b/pkgs/development/libraries/science/math/openblas/default.nix @@ -76,11 +76,10 @@ let if blas64_ != null then blas64_ else hasPrefix "x86_64" stdenv.system; - - version = "0.3.0"; in -stdenv.mkDerivation { +stdenv.mkDerivation rec { name = "openblas-${version}"; + version = "0.3.0"; src = fetchurl { url = "https://github.com/xianyi/OpenBLAS/archive/v${version}.tar.gz"; sha256 = "18giv3lsh8cva01z4rhsx8jvgliknni0jp7vxkc69qxb14vm8lfg"; diff --git a/pkgs/development/libraries/science/math/rankwidth/default.nix b/pkgs/development/libraries/science/math/rankwidth/default.nix index f38fce5831ee..fda54fe44ab1 100644 --- a/pkgs/development/libraries/science/math/rankwidth/default.nix +++ b/pkgs/development/libraries/science/math/rankwidth/default.nix @@ -8,7 +8,7 @@ stdenv.mkDerivation rec { name = "${pname}-${version}"; src = fetchurl { - url = "http://mirrors.mit.edu/sage/spkg/upstream/rw/rw-${version}.tar.gz"; + url = "mirror://sageupstream/rw/rw-${version}.tar.gz"; sha256 = "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"; }; diff --git a/pkgs/development/libraries/science/math/rubiks/default.nix b/pkgs/development/libraries/science/math/rubiks/default.nix index fe448106b15d..624885c501aa 100644 --- a/pkgs/development/libraries/science/math/rubiks/default.nix +++ b/pkgs/development/libraries/science/math/rubiks/default.nix @@ -10,7 +10,7 @@ stdenv.mkDerivation rec { name = "${pname}-${version}"; src = fetchurl { - url = "http://mirrors.mit.edu/sage/spkg/upstream/rubiks/rubiks-${version}.tar.bz2"; + url = "mirror://sageupstream/rubiks/rubiks-${version}.tar.bz2"; sha256 = "0zdmkb0j1kyspdpsszzb2k3279xij79jkx0dxd9f3ix1yyyg3yfq"; }; diff --git a/pkgs/development/libraries/science/math/sympow/default.nix b/pkgs/development/libraries/science/math/sympow/default.nix index c83b3d1737cf..c34701e3f913 100644 --- a/pkgs/development/libraries/science/math/sympow/default.nix +++ b/pkgs/development/libraries/science/math/sympow/default.nix @@ -10,7 +10,7 @@ stdenv.mkDerivation rec { src = fetchurl { # Original website no longer reachable - url = "http://mirrors.mit.edu/sage/spkg/upstream/sympow/sympow-${version}.tar.bz2"; + url = "mirror://sageupstream/sympow/sympow-${version}.tar.bz2"; sha256 = "0hphs7ia1wr5mydf288zvwj4svrymfpadcg3pi6w80km2yg5bm3c"; }; @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { installPhase = '' runHook preInstall - install -d datafiles "$out/share/sympow/datafiles" + install -D datafiles/* --target-directory "$out/share/sympow/datafiles/" install *.gp "$out/share/sympow/" install -Dm755 sympow "$out/share/sympow/sympow" install -D new_data "$out/bin/new_data" diff --git a/pkgs/development/libraries/tachyon/default.nix b/pkgs/development/libraries/tachyon/default.nix index 53e48eb89317..0185bd2733b4 100644 --- a/pkgs/development/libraries/tachyon/default.nix +++ b/pkgs/development/libraries/tachyon/default.nix @@ -38,6 +38,7 @@ stdenv.mkDerivation rec { arch = if stdenv.system == "x86_64-linux" then "linux-64-thr" else if stdenv.system == "i686-linux" then "linux-thr" else if stdenv.system == "aarch64-linux" then "linux-arm-thr" else + if stdenv.system == "armv7l-linux" then "linux-arm-thr" else if stdenv.system == "x86_64-darwin" then "macosx-thr" else if stdenv.system == "i686-darwin" then "macosx-64-thr" else if stdenv.system == "i686-cygwin" then "win32" else diff --git a/pkgs/development/python-modules/cysignals/default.nix b/pkgs/development/python-modules/cysignals/default.nix index 56d997c6b325..dc88c4d94f7a 100644 --- a/pkgs/development/python-modules/cysignals/default.nix +++ b/pkgs/development/python-modules/cysignals/default.nix @@ -2,9 +2,11 @@ , fetchPypi , buildPythonPackage , cython -, sphinx +, pariSupport ? true, pari # for interfacing with the PARI/GP signal handler }: +assert pariSupport -> pari != null; + buildPythonPackage rec { pname = "cysignals"; version = "1.7.1"; @@ -14,6 +16,8 @@ buildPythonPackage rec { sha256 = "15nky8siwlc7s8v23vv4m0mnxa1z6jcs2qfr26m2mkw9j9g2na2j"; }; + # explicit check: + # build/src/cysignals/implementation.c:27:2: error: #error "cysignals must be compiled without _FORTIFY_SOURCE" hardeningDisable = [ "fortify" ]; @@ -26,6 +30,10 @@ buildPythonPackage rec { export PATH="$out/bin:$PATH" ''; + buildInputs = lib.optionals pariSupport [ + pari + ]; + propagatedBuildInputs = [ cython ]; diff --git a/pkgs/development/python-modules/flask-autoindex/default.nix b/pkgs/development/python-modules/flask-autoindex/default.nix index 95e457de81d3..f36d7fbca1c4 100644 --- a/pkgs/development/python-modules/flask-autoindex/default.nix +++ b/pkgs/development/python-modules/flask-autoindex/default.nix @@ -1,7 +1,6 @@ { stdenv , buildPythonPackage -, fetchpatch -, fetchPypi +, fetchFromGitHub , flask , flask-silk , future @@ -9,11 +8,16 @@ buildPythonPackage rec { pname = "Flask-AutoIndex"; - version = "0.6"; + version = "2018-06-28"; - src = fetchPypi { - inherit pname version; - sha256 = "19b10mb1nrqfjyafki6wnrbn8mqi30bbyyiyvp5xssc74pciyfqs"; + # master fixes various issues (binary generation, flask syntax) and has no + # major changes + # new release requested: https://github.com/sublee/flask-autoindex/issues/38 + src = fetchFromGitHub { + owner = "sublee"; + repo = "flask-autoindex"; + rev = "e3d449a89d56bf4c171c7c8d90af028e579782cf"; + sha256 = "0bwq2nid4h8vrxspggk064vra4wd804cl2ryyx4j2d1dyywmgjgy"; }; propagatedBuildInputs = [ @@ -22,15 +26,6 @@ buildPythonPackage rec { future ]; - patches = [ - # fix generated binary, see https://github.com/sublee/flask-autoindex/pull/32 - (fetchpatch { - name = "fix_binary.patch"; - url = "https://github.com/sublee/flask-autoindex/pull/32.patch"; - sha256 = "1v2r0wvi7prhipjq89774svv6aqj0a13mdfj07pdlkpzfbf029dn"; - }) - ]; - meta = with stdenv.lib; { description = "The mod_autoindex for Flask"; longDescription = '' diff --git a/pkgs/development/python-modules/flask-silk/default.nix b/pkgs/development/python-modules/flask-silk/default.nix index e494f22a4762..edc873458a11 100644 --- a/pkgs/development/python-modules/flask-silk/default.nix +++ b/pkgs/development/python-modules/flask-silk/default.nix @@ -1,16 +1,20 @@ { stdenv , buildPythonPackage -, fetchPypi +, fetchFromGitHub , flask }: buildPythonPackage rec { pname = "Flask-Silk"; - version = "0.2"; + version = "2018-06-28"; - src = fetchPypi { - inherit pname version; - sha256 = "1gjzighx4f0w39sq9xvzr1kwb4y7yv9qrgzvli1p89gy16piz8l0"; + # master fixes flask import syntax and has no major changes + # new release requested: https://github.com/sublee/flask-silk/pull/6 + src = fetchFromGitHub { + owner = "sublee"; + repo = "flask-silk"; + rev = "3a8166550f9a0ec52edae7bf31d9818c4c15c531"; + sha256 = "0mplziqw52jfspas6vsm210lmxqqzgj0dxm8y0i3gpbyyykwcmh0"; }; propagatedBuildInputs = [ diff --git a/pkgs/development/python-modules/sympy/default.nix b/pkgs/development/python-modules/sympy/default.nix index 67c799e554eb..f41f2e7b4fa1 100644 --- a/pkgs/development/python-modules/sympy/default.nix +++ b/pkgs/development/python-modules/sympy/default.nix @@ -1,6 +1,7 @@ { lib , buildPythonPackage , fetchPypi +, fetchpatch , glibcLocales , mpmath }: @@ -25,10 +26,26 @@ buildPythonPackage rec { export LANG="en_US.UTF-8" ''; + patches = [ + # see https://trac.sagemath.org/ticket/20204 and https://github.com/sympy/sympy/issues/12825 + # There is also an upstream patch for this, included in the next release (PR #128826). + # However that doesn't quite fix the issue yet. Apparently some changes by sage are required. + # TODO re-evaluate the change once a new sympy version is released (open a sage trac ticket about + # it). + (fetchpatch { + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/sympy/patches/03_undeffun_sage.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "1mh2va1rlgizgvx8yzqwgvbf5wvswarn511002b361mc8yy0bnhr"; + }) + (fetchpatch { + url = "https://github.com/sympy/sympy/pull/13276.patch"; + sha256 = "1rz74b5c74vwh3pj9axxgh610i02l3555vvsvr4a15ya7siw7zxh"; + }) + ]; + meta = { description = "A Python library for symbolic mathematics"; homepage = http://www.sympy.org/; license = lib.licenses.bsd3; maintainers = with lib.maintainers; [ lovek323 ]; }; -} \ No newline at end of file +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index a43f04e9411d..54978fd37866 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -10099,6 +10099,24 @@ with pkgs; libgadu = callPackage ../development/libraries/libgadu { }; + gap-libgap-compatible = let + version = "4r8p6"; + pkgVer = "2016_11_12-14_25"; + in + (gap.override { keepAllPackages = false; }).overrideAttrs (oldAttrs: { + name = "libgap-${oldAttrs.pname}-${version}"; + src = fetchurl { + url = "https://www.gap-system.org/pub/gap/gap48/tar.bz2/gap${version}_${pkgVer}.tar.bz2"; + sha256 = "19n2p1mdg33s2x9rs51iak7rgndc1cwr56jyqnah0g1ydgg1yh6b"; + }; + patches = (oldAttrs.patches or []) ++ [ + # don't install any packages by default (needed for interop with libgap, probably obsolete with 4r10 + (fetchpatch { + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/gap/patches/nodefaultpackages.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "1xwj766m3axrxbkyx13hy3q8s2wkqxy3m6mgpwq3c3n4vk3v416v"; + }) + ]; + }); libgap = callPackage ../development/libraries/libgap { }; libgdata = gnome3.libgdata; @@ -14586,18 +14604,26 @@ with pkgs; camingo-code = callPackage ../data/fonts/camingo-code { }; + combinatorial_designs = callPackage ../data/misc/combinatorial_designs { }; + + conway_polynomials = callPackage ../data/misc/conway_polynomials { }; + dosis = callPackage ../data/fonts/dosis { }; dosemu_fonts = callPackage ../data/fonts/dosemu-fonts { }; eb-garamond = callPackage ../data/fonts/eb-garamond { }; + elliptic_curves = callPackage ../data/misc/elliptic_curves { }; + faba-icon-theme = callPackage ../data/icons/faba-icon-theme { }; faba-mono-icons = callPackage ../data/icons/faba-mono-icons { }; fixedsys-excelsior = callPackage ../data/fonts/fixedsys-excelsior { }; + graphs = callPackage ../data/misc/graphs { }; + emacs-all-the-icons-fonts = callPackage ../data/fonts/emacs-all-the-icons-fonts { }; emojione = callPackage ../data/fonts/emojione { @@ -14802,8 +14828,14 @@ with pkgs; paratype-pt-sans = callPackage ../data/fonts/paratype-pt/sans.nix {}; paratype-pt-serif = callPackage ../data/fonts/paratype-pt/serif.nix {}; + pari-galdata = callPackage ../data/misc/pari-galdata {}; + + pari-seadata-small = callPackage ../data/misc/pari-seadata-small {}; + poly = callPackage ../data/fonts/poly { }; + polytopes_db = callPackage ../data/misc/polytopes_db { }; + posix_man_pages = callPackage ../data/documentation/man-pages-posix { }; powerline-fonts = callPackage ../data/fonts/powerline-fonts { }; @@ -20351,7 +20383,10 @@ with pkgs; petsc = callPackage ../development/libraries/science/math/petsc { }; - sage = callPackage ../applications/science/math/sage { }; + sage = callPackage ../applications/science/math/sage { + nixpkgs = pkgs; + }; + sageWithDoc = sage.override { withDoc = true; }; suitesparse_4_2 = callPackage ../development/libraries/science/math/suitesparse/4.2.nix { }; suitesparse_4_4 = callPackage ../development/libraries/science/math/suitesparse {};