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sage: 8.1 -> 8.2, use system packages
This commit is contained in:
Timo Kaufmann
parent
84d89a1ec6
commit
17e6b391eb
37 changed files with 2695 additions and 413 deletions
117
pkgs/applications/science/math/sage/README.md
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117
pkgs/applications/science/math/sage/README.md
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@ -0,0 +1,117 @@
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# Sage on nixos
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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.
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Don't feel discouraged to fix, simplify or improve things though. Here's a quick overview over the functions of the individual files:
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- `sage-src.nix`
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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.
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- `env-locations.nix`
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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`).
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- `sage-env.nix`
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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.
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- `sagelib.nix`
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Defines the main sage package (without setting the necessary environments or running any tests).
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- `sage-with-env.nix`
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Wraps sage in the necessary environment.
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- `sage.nix`
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Runs sages doctests.
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- `sage-wrapper.nix`
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Optionally tells sage where do find the docs.
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- `sagedoc.nix`
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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.
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- `sagenb.nix`
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The (semi deprecated) sage notebook.
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- `default.nix`
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Introduces necessary overrides, defines new packages and ties everything together (returning the `sage` package).
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- `flask-oldsessions.nix`, `flask-openid.nix`, `python-openid.nix`
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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.
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- `pybrial.nix`
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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.
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- `openblas-pc.nix`
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This creates a `.pc` file to be read by `pkg-config` that allows openblas to take on different roles, like `cblas` or `lapack`.
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## The sage build is broken
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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).
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If the build broke as a result of a package update, try those solutions in order:
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- search the [sage trac](https://trac.sagemath.org/) for keywords like "Upgrade <package>". Maybe somebody has already proposed a patch that fixes the issue. You can then add a `fetchpatch` to `sage-src.nix`.
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- 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).
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- fix the problem yourself. First clone the sagemath source and then check out the sage version you want to patch:
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```
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[user@localhost ~]$ git clone git://github.com/sagemath/sage.git
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[user@localhost ~]$ cd sage
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[user@localhost sage]$ git checkout 8.2 # substitute the relevant version here
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```
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Then make the needed changes and generate a patch with `git diff`:
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```
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[user@localhost ~]$ <make changes>
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[user@localhost ~]$ git diff -u > /path/to/nixpkgs/pkgs/applications/science/math/sage/patches/name-of-patch.patch
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```
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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.
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- pin the package version in `default.nix` and add a note that explains why that is necessary.
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## Proposing a sage patch
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You can [login the sage trac using GitHub](https://trac.sagemath.org/login). Your username will then be `gh-<your-github-name>`. 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.
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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:
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```
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[user@localhost ~]$ git clone git://github.com/sagemath/sage.git
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[user@localhost ~]$ cd sage
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[user@localhost sage]$ git remote add trac git@trac.sagemath.org:sage.git -t master
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[user@localhost sage]$ git checkout -b u/gh-<your-github-username>/<your-branch-name> develop
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[user@localhost sage]$ <make changes>
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[user@localhost sage]$ git add .
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[user@localhost sage]$ git commit
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[user@localhost sage]$ git show # review your changes
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[user@localhost sage]$ git push --set-upstream trac u/gh-<your-github-username>/<your-branch-name>
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```
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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-<your-github-username>/` prefix).
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Now you can [create a new trac ticket](https://trac.sagemath.org/newticket).
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- Write a description of the change
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- set the type and component as appropriate
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- write your real name in the "Authors" field
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- write `u/gh-<your-github-username>/<your-branch-name>` in the "Branch" field
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- click "Create ticket"
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- click "Modify" on the top right of your ticket (for some reason you can only change the ticket status after you have created it)
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- set the ticket status from `new` to `needs_review`
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- click "Save changes"
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Refer to sages [Developer's Guide](http://doc.sagemath.org/html/en/developer/index.html) for further details.
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## I want to update sage
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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.
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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).
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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.
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## Well, that didn't help!
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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).
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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!
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@ -1,230 +1,231 @@
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# TODO
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# - consider writing a script to convert spkgs to nix packages, similar to vim
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# or cabal2nix. This would allow a more efficient and "cleaner" build, greater
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# flexibility and the possibility to select which dependencies to add and which
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# to remove. It would also allow to use system packages for some dependencies
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# and recompile others (optimized for the system) without recompiling everything.
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# - add optdeps:
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# - imagemagick
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# - texlive full for documentation
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# - ...
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# - further seperate build outputs. Also maybe run `make doc`.
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# Configure flags like --bindir and --libdir oculd also be used for that, see
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# ./configure --help`.
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# Other resources:
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# - https://wiki.debian.org/DebianScience/Sage
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# - https://github.com/cschwan/sage-on-gentoo
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# - https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath
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{ stdenv
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, bash
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, fetchurl
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, perl
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, gfortran6
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, python
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, autoreconfHook
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, gettext
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, which
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, texlive
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, texinfo
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, hevea
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, buildDocs ? false
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, optimize ? false # optimize sage to the current system (obviously impure)
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{ nixpkgs
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, withDoc ? false
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}:
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stdenv.mkDerivation rec {
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version = "8.1";
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name = "sage-${version}";
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let
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inherit (nixpkgs) fetchpatch fetchurl symlinkJoin fetchFromGitHub callPackage nodePackages_8_x;
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# Modified version of patchShebangs that patches to the sage-internal version if possible
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# and falls back to the system version if not.
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patchSageShebangs = ./patchSageShebangs.sh;
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src = fetchurl {
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# Note that the source is *not* fetched from github, since that doesn't
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# the upstream folder with all the source tarballs of the spkgs.
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# If those are not present they are fetched at build time, which breaks
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# when building in a sandbox (and probably only works if you install the
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# latest sage version).
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urls = [
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"http://mirrors.mit.edu/sage/src/sage-${version}.tar.gz"
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"ftp://ftp.fu-berlin.de/unix/misc/sage/src/sage-${version}.tar.gz"
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"http://sagemath.polytechnic.edu.na/src/sage-${version}.tar.gz"
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"ftp://ftp.sun.ac.za/pub/mirrors/www.sagemath.org/src/sage-${version}.tar.gz"
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"http://sagemath.mirror.ac.za/src/sage-${version}.tar.gz"
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"https://ftp.leg.uct.ac.za/pub/packages/sage/src/sage-${version}.tar.gz"
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"http://mirror.ufs.ac.za/sagemath/src/sage-${version}.tar.gz"
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"https://mirrors-usa.go-parts.com/sage/sagemath/src/sage-${version}.tar.gz"
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"http://www.cecm.sfu.ca/sage/src/sage-${version}.tar.gz"
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"http://files.sagemath.org/src/sage-${version}.tar.gz"
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"https://mirrors.xmission.com/sage/src/sage-${version}.tar.gz"
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"http://sagemath.c3sl.ufpr.br/src/sage-${version}.tar.gz"
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"http://linorg.usp.br/sage/src/sage-${version}.tar.gz"
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"http://mirror.hust.edu.cn/sagemath/src/sage-${version}.tar.gz"
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"https://ftp.iitm.ac.in/sage/src/sage-${version}.tar.gz"
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"http://ftp.kaist.ac.kr/sage/src/sage-${version}.tar.gz"
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"https://ftp.riken.jp/sagemath/src/sage-${version}.tar.gz"
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"https://mirrors.tuna.tsinghua.edu.cn/sagemath/src/sage-${version}.tar.gz"
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"https://mirrors.ustc.edu.cn/sagemath/src/sage-${version}.tar.gz"
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"http://ftp.tsukuba.wide.ad.jp/software/sage/src/sage-${version}.tar.gz"
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"https://ftp.yz.yamagata-u.ac.jp/pub/math/sage/src/sage-${version}.tar.gz"
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"https://mirror.yandex.ru/mirrors/sage.math.washington.edu/src/sage-${version}.tar.gz"
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"https://mirror.aarnet.edu.au/pub/sage/src/sage-${version}.tar.gz"
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"https://sage.mirror.garr.it/mirrors/sage/src/sage-${version}.tar.gz"
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"https://www.mirrorservice.org/sites/www.sagemath.org/src/sage-${version}.tar.gz"
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"http://mirror.switch.ch/mirror/sagemath/src/sage-${version}.tar.gz"
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"https://mirrors.up.pt/pub/sage/src/sage-${version}.tar.gz"
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"http://www-ftp.lip6.fr/pub/math/sagemath/src/sage-${version}.tar.gz"
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"http://ftp.ntua.gr/pub/sagemath/src/sage-${version}.tar.gz"
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# https://trac.sagemath.org/ticket/15980 for tracking of python3 support
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python = nixpkgs.python2.override {
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packageOverrides = self: super: {
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cypari2 = super.cypari2.override { inherit pari; };
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cysignals = super.cysignals.override { inherit pari; };
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cvxopt = super.cvxopt.override { inherit glpk; };
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# https://github.com/sagemath/sagenb/issues/437
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flask-babel = super.flask-babel.overridePythonAttrs (attrs: rec {
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version = "0.9";
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src = attrs.src.override {
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inherit version;
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sha256 = "0k7vk4k54y55ma0nx2k5s0phfqbriwslhy5shh3b0d046q7ibzaa";
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};
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doCheck = false;
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});
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# python packages that appear unmaintained and were not accepted into the nixpkgs
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# tree because of that. These packages are only dependencies of the more-or-less
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# deprecated sagenb. However sagenb is still a default dependency and the doctests
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# depend on it.
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# See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion.
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flask-oldsessions = self.callPackage ./flask-oldsessions.nix {};
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flask-openid = self.callPackage ./flask-openid.nix {};
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python-openid = self.callPackage ./python-openid.nix {};
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pybrial = self.callPackage ./pybrial.nix {};
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sagelib = self.callPackage ./sagelib.nix {
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inherit flint ecl pari glpk eclib;
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inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
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linbox = nixpkgs.linbox.override { withSage = true; };
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# tracking: https://trac.sagemath.org/ticket/24927
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arb = nixpkgs.arb.overrideAttrs (attrs: rec {
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name = "arb-${version}";
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version = "2.12.0";
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doCheck = false; # https://github.com/fredrik-johansson/arb/issues/194
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src = fetchFromGitHub {
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owner = "fredrik-johansson";
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repo = attrs.pname;
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rev = version;
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sha256 = "18bwxlcbqb70cj7l9x6w1h4yghrqfhmbhdby373q8vdrdfx58niq";
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};
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});
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};
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sagenb = self.callPackage ./sagenb.nix {
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mathjax = nodePackages_8_x.mathjax;
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};
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sagedoc = self.callPackage ./sagedoc.nix {
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inherit sage-src;
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};
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env-locations = self.callPackage ./env-locations.nix {
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inherit pari_data ecl pari;
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inherit singular;
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three = nodePackages_8_x.three;
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mathjax = nodePackages_8_x.mathjax;
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};
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sage-env = self.callPackage ./sage-env.nix {
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inherit sage-src python rWrapper openblas-cblas-pc glpk ecl singular eclib pari palp flint pynac pythonEnv;
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pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
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};
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sage-with-env = self.callPackage ./sage-with-env.nix {
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inherit pari eclib pythonEnv;
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inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
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pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
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three = nodePackages_8_x.three;
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};
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sage = self.callPackage ./sage.nix { };
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sage-wrapper = self.callPackage ./sage-wrapper.nix {
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inherit sage-src withDoc;
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};
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};
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};
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openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; };
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openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; };
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openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; };
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|
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sage-src = callPackage ./sage-src.nix {};
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pythonRuntimeDeps = with python.pkgs; [
|
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sagelib
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pybrial
|
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sagenb
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cvxopt
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networkx
|
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service-identity
|
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psutil
|
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sympy
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fpylll
|
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matplotlib
|
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scipy
|
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ipywidgets
|
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rpy2
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sphinx
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typing
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pillow
|
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];
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pythonEnv = python.buildEnv.override {
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extraLibs = pythonRuntimeDeps;
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ignoreCollisions = true;
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} // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
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# needs to be rWrapper, standard "R" doesn't include default packages
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rWrapper = nixpkgs.rWrapper.override {
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# https://trac.sagemath.org/ticket/25674
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R = nixpkgs.R.overrideAttrs (attrs: rec {
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name = "R-3.4.4";
|
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src = fetchurl {
|
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url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
|
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sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk";
|
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};
|
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});
|
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};
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|
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# update causes issues
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# https://groups.google.com/forum/#!topic/sage-packaging/cS3v05Q0zso
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# https://trac.sagemath.org/ticket/24735
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singular = nixpkgs.singular.overrideAttrs (oldAttrs: {
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name = "singular-4.1.0p3";
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src = fetchurl {
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url = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/4-1-0/singular-4.1.0p3.tar.gz";
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sha256 = "105zs3zk46b1cps403ap9423rl48824ap5gyrdgmg8fma34680a4";
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};
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});
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# *not* to confuse with the python package "pynac"
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# https://trac.sagemath.org/ticket/24838 (depends on arb update)
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pynac = (nixpkgs.pynac.override { inherit singular; }).overrideAttrs (oldAttrs: rec {
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name = "pynac-0.7.16";
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src = fetchFromGitHub {
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owner = "pynac";
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repo = "pynac";
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rev = name;
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sha256 = "106an189sg4rpgzfrmy3699271vg4ddazw9wvh51wx7qnm1v86ik";
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};
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});
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eclib = nixpkgs.eclib.override { inherit pari; };
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# With openblas (64 bit), the tests fail the same way as when sage is build with
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# openblas instead of openblasCompat. Apparently other packages somehow use flints
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# blas when it is available. Alternative would be to override flint to use
|
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# 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;
|
||||
}
|
||||
|
|
|
|||
46
pkgs/applications/science/math/sage/env-locations.nix
Normal file
46
pkgs/applications/science/math/sage/env-locations.nix
Normal file
|
|
@ -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"
|
||||
'';
|
||||
}
|
||||
|
|
@ -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.
|
||||
|
|
@ -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-${version}.tar.gz/'
|
||||
36
pkgs/applications/science/math/sage/flask-oldsessions.nix
Normal file
36
pkgs/applications/science/math/sage/flask-oldsessions.nix
Normal file
|
|
@ -0,0 +1,36 @@
|
|||
{ stdenv
|
||||
, buildPythonPackage
|
||||
, fetchFromGitHub
|
||||
, python
|
||||
, flask
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "Flask-OldSessions";
|
||||
version = "0.10";
|
||||
|
||||
# no artifact on pypi: https://github.com/mitsuhiko/flask-oldsessions/issues/1
|
||||
src = fetchFromGitHub {
|
||||
owner = "mitsuhiko";
|
||||
repo = "flask-oldsessions";
|
||||
rev = "${version}";
|
||||
sha256 = "04b5m8njjiwld9a0zw55iqwvyjgwcpdbhz1cic8nyhgcmypbicqn";
|
||||
};
|
||||
|
||||
propagatedBuildInputs = [
|
||||
flask
|
||||
];
|
||||
|
||||
# missing module flask.testsuite, probably assumes an old version of flask
|
||||
doCheck = false;
|
||||
checkPhase = ''
|
||||
${python.interpreter} run-tests.py
|
||||
'';
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
description = "Provides a session class that works like the one in Flask before 0.10.";
|
||||
license = licenses.bsd2;
|
||||
maintainers = with maintainers; [ timokau ];
|
||||
homepage = https://github.com/mitsuhiko/flask-oldsessions;
|
||||
};
|
||||
}
|
||||
28
pkgs/applications/science/math/sage/flask-openid.nix
Normal file
28
pkgs/applications/science/math/sage/flask-openid.nix
Normal file
|
|
@ -0,0 +1,28 @@
|
|||
{ stdenv
|
||||
, buildPythonPackage
|
||||
, fetchPypi
|
||||
, flask
|
||||
, python-openid
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "Flask-OpenID";
|
||||
version = "1.2.5";
|
||||
|
||||
src = fetchPypi {
|
||||
inherit pname version;
|
||||
sha256 = "1aycwmwi7ilcaa5ab8hm0bp6323zl8z25q9ha0gwrl8aihfgx3ss";
|
||||
};
|
||||
|
||||
propagatedBuildInputs = [
|
||||
flask
|
||||
python-openid
|
||||
];
|
||||
|
||||
meta = with stdenv.lib; {
|
||||
description = "Adds openid support to flask applications";
|
||||
license = licenses.bsd2;
|
||||
maintainers = with maintainers; [ timokau ];
|
||||
homepage = https://pythonhosted.org/Flask-OpenID/;
|
||||
};
|
||||
}
|
||||
18
pkgs/applications/science/math/sage/openblas-pc.nix
Normal file
18
pkgs/applications/science/math/sage/openblas-pc.nix
Normal file
|
|
@ -0,0 +1,18 @@
|
|||
{ stdenv
|
||||
, openblasCompat
|
||||
, writeTextFile
|
||||
, name
|
||||
}:
|
||||
|
||||
writeTextFile {
|
||||
name = "openblas-${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
|
||||
'';
|
||||
}
|
||||
|
|
@ -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
|
||||
|
|
@ -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)
|
||||
<li><a class="reference external" href="../reference/padics/sage/rings/padics/tutorial.html#sage-rings-padics-tutorial" title="(in Sage Reference Manual: p-Adics ...)"><span>Introduction to the -adics</span></a></li>
|
||||
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")
|
||||
|
|
@ -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]]'
|
||||
|
|
@ -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.')
|
||||
|
|
@ -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)
|
||||
|
||||
812
pkgs/applications/science/math/sage/patches/numpy-1.14.3.patch
Normal file
812
pkgs/applications/science/math/sage/patches/numpy-1.14.3.patch
Normal file
|
|
@ -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.]],
|
||||
<BLANKLINE>
|
||||
- [[ 1., 1., 1.],
|
||||
- [ 0., 0., 0.],
|
||||
- [ 1., 1., 1.]],
|
||||
+ [[1., 1., 1.],
|
||||
+ [0., 0., 0.],
|
||||
+ [1., 1., 1.]],
|
||||
<BLANKLINE>
|
||||
- [[ 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. ]],
|
||||
<BLANKLINE>
|
||||
- [[ 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. ]],
|
||||
<BLANKLINE>
|
||||
- [[ 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)
|
||||
- <BLANKLINE>
|
||||
+ 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
|
||||
|
||||
|
|
@ -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):
|
||||
<type 'float'>
|
||||
"""
|
||||
got = self.human_readable_escape_sequences(got)
|
||||
+ got = pari_stack_warning_regex.sub('', got)
|
||||
if isinstance(want, MarkedOutput):
|
||||
if want.random:
|
||||
return True
|
||||
|
|
@ -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
|
||||
|
|
@ -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('<sage_test>', 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,
|
||||
|
|
@ -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
|
||||
"""
|
||||
|
|
@ -0,0 +1,31 @@
|
|||
From 7419e0246230594ebfd5e7a2fe6b80d67abfc98a Mon Sep 17 00:00:00 2001
|
||||
From: Jeroen Demeyer <jdemeyer@cage.ugent.be>
|
||||
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')
|
||||
- '...<div class="docstring">\n \n <p>A test</p>\n\n\n</div>'
|
||||
+ '<div class="docstring">\n \n <p>A test</p>\n\n\n</div>'
|
||||
sage: sphinxify('**Testing**\n`monospace`')
|
||||
- '...<div class="docstring"...<strong>Testing</strong>\n<span class="math"...</p>\n\n\n</div>'
|
||||
+ '<div class="docstring"...<strong>Testing</strong>\n<span class="math notranslate"...</p>\n\n\n</div>'
|
||||
sage: sphinxify('`x=y`')
|
||||
- '...<div class="docstring">\n \n <p><span class="math">x=y</span></p>\n\n\n</div>'
|
||||
+ '<div class="docstring">\n \n <p><span class="math notranslate">x=y</span></p>\n\n\n</div>'
|
||||
sage: sphinxify('`x=y`', format='text')
|
||||
'x=y\n'
|
||||
sage: sphinxify(':math:`x=y`', format='text')
|
||||
--
|
||||
cgit v1.0-1-gd88e
|
||||
|
||||
62
pkgs/applications/science/math/sage/patches/sphinx-1.7.patch
Normal file
62
pkgs/applications/science/math/sage/patches/sphinx-1.7.patch
Normal file
|
|
@ -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 "$@" </dev/null
|
||||
fi
|
||||
|
||||
if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
|
||||
diff --git a/src/doc/common/conf.py b/src/doc/common/conf.py
|
||||
index 25f94f7b7d..3f07474d9b 100644
|
||||
--- a/src/doc/common/conf.py
|
||||
+++ b/src/doc/common/conf.py
|
||||
@@ -627,7 +627,7 @@ def call_intersphinx(app, env, node, contnode):
|
||||
sage: for line in open(thematic_index).readlines():
|
||||
....: if "padics" in line:
|
||||
....: sys.stdout.write(line)
|
||||
- <li><a class="reference external" href="../reference/padics/sage/rings/padics/tutorial.html#sage-rings-padics-tutorial" title="(in Sage Reference Manual: p-Adics ...)"><span>Introduction to the -adics</span></a></li>
|
||||
+ <li><a class="reference external" href="../reference/padics/sage/rings/padics/tutorial.html#sage-rings-padics-tutorial" title="(in Sage Reference Manual: p-Adics v...)"><span>Introduction to the -adics</span></a></li>
|
||||
"""
|
||||
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')
|
||||
- '...<div class="docstring">\n \n <p>A test</p>\n\n\n</div>'
|
||||
+ '<div class="docstring">\n \n <p>A test</p>\n\n\n</div>'
|
||||
sage: sphinxify('**Testing**\n`monospace`')
|
||||
- '...<div class="docstring"...<strong>Testing</strong>\n<span class="math"...</p>\n\n\n</div>'
|
||||
+ '<div class="docstring"...<strong>Testing</strong>\n<span class="math...</p>\n\n\n</div>'
|
||||
sage: sphinxify('`x=y`')
|
||||
- '...<div class="docstring">\n \n <p><span class="math">x=y</span></p>\n\n\n</div>'
|
||||
+ '<div class="docstring">\n \n <p><span class="math notranslate nohighlight">x=y</span></p>\n\n\n</div>'
|
||||
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
|
||||
|
|
@ -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()}
|
||||
|
||||
29
pkgs/applications/science/math/sage/pybrial.nix
Normal file
29
pkgs/applications/science/math/sage/pybrial.nix
Normal file
|
|
@ -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 ];
|
||||
};
|
||||
}
|
||||
42
pkgs/applications/science/math/sage/python-openid.nix
Normal file
42
pkgs/applications/science/math/sage/python-openid.nix
Normal file
|
|
@ -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/;
|
||||
};
|
||||
}
|
||||
162
pkgs/applications/science/math/sage/sage-env.nix
Normal file
162
pkgs/applications/science/math/sage/sage-env.nix
Normal file
|
|
@ -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"
|
||||
'';
|
||||
}
|
||||
197
pkgs/applications/science/math/sage/sage-src.nix
Normal file
197
pkgs/applications/science/math/sage/sage-src.nix
Normal file
|
|
@ -0,0 +1,197 @@
|
|||
{ stdenv
|
||||
, fetchFromGitHub
|
||||
, fetchpatch
|
||||
}:
|
||||
stdenv.mkDerivation rec {
|
||||
version = "8.2";
|
||||
name = "sage-src-${version}";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "sagemath";
|
||||
repo = "sage";
|
||||
rev = version;
|
||||
sha256 = "0d7vc16s7dj23an2cb8v5bhbnc6nsw20qhnnxr0xh8qg629027b8";
|
||||
};
|
||||
|
||||
nixPatches = [
|
||||
# https://trac.sagemath.org/ticket/25309
|
||||
(fetchpatch {
|
||||
name = "spkg-paths.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch/?h=97f06fddee920399d4fcda65aa9b0925774aec69&id=a86151429ccce1ddd085e8090ada8ebdf02f3310";
|
||||
sha256 = "1xb9108rzzkdhn71vw44525620d3ww9jv1fph5a77v9y7nf9wgr7";
|
||||
})
|
||||
(fetchpatch {
|
||||
name = "maxima-fas.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch/?h=97f06fddee920399d4fcda65aa9b0925774aec69";
|
||||
sha256 = "14s50yg3hpw9cp3v581dx7zfmpm2j972im7x30iwki8k45mjvk3i";
|
||||
})
|
||||
|
||||
# https://trac.sagemath.org/ticket/25328
|
||||
(fetchpatch {
|
||||
name = "respect-jupyter-path.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=029123097d79f2c67bca2d725c470ef667a88ca2";
|
||||
sha256 = "0qw9p541ip0kn2gfvn4i05a06p50f3q46847gqfjjgzxhn62znfw";
|
||||
})
|
||||
|
||||
# https://trac.sagemath.org/ticket/25358
|
||||
(fetchpatch {
|
||||
name = "safe-directory-test-without-patch.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=dc673c17555efca611f68398d5013b66e9825463";
|
||||
sha256 = "1hhannz7xzprijakn2w2d0rhd5zv2zikik9p51i87bas3nc658f7";
|
||||
})
|
||||
|
||||
# https://trac.sagemath.org/ticket/25357 rebased on 8.2
|
||||
./patches/python3-syntax-without-write.patch
|
||||
|
||||
# https://trac.sagemath.org/ticket/25314
|
||||
(fetchpatch {
|
||||
name = "make-qepcad-test-optional.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch/?h=fe294c58bd035ef427e268901d54a6faa0058138";
|
||||
sha256 = "003d5baf5c0n5rfg010ijwkwz8kg0s414cxwczs2vhdayxdixbix";
|
||||
})
|
||||
|
||||
# https://trac.sagemath.org/ticket/25316
|
||||
./patches/python-5755-hotpatch.patch
|
||||
|
||||
# https://trac.sagemath.org/ticket/25354
|
||||
# https://trac.sagemath.org/ticket/25531
|
||||
(fetchpatch {
|
||||
name = "cysignals-include.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch/?h=28778bd25a37c80884d2b24e0683fb2989300cef";
|
||||
sha256 = "0fiiiw91pgs8avm9ggj8hb64bhqzl6jcw094d94nhirmh8w2jmc5";
|
||||
})
|
||||
|
||||
# https://trac.sagemath.org/ticket/25315
|
||||
(fetchpatch {
|
||||
name = "find-libraries-in-dyld-library-path.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch/?h=20d4593876ce9c6004eac2ab6fd61786d0d96a06";
|
||||
sha256 = "1k3afq3qlzmgqwx6rzs5wv153vv9dsf5rk8pi61g57l3r3npbjmc";
|
||||
})
|
||||
|
||||
# Pari upstream has since accepted a patch, so this patch won't be necessary once sage updates pari.
|
||||
# https://trac.sagemath.org/ticket/25312
|
||||
./patches/pari-stackwarn.patch
|
||||
|
||||
# https://trac.sagemath.org/ticket/25311
|
||||
./patches/zn_poly_version.patch
|
||||
|
||||
# https://trac.sagemath.org/ticket/25345
|
||||
# (upstream patch doesn't apply on 8.2 source)
|
||||
./patches/dochtml-optional.patch
|
||||
];
|
||||
|
||||
packageUpgradePatches = [
|
||||
# matplotlib 2.2.2 deprecated `normed` (replaced by `density`).
|
||||
# This patch only ignores the warning. It would be equally easy to fix it
|
||||
# (by replacing all mentions of `normed` by `density`), but its better to
|
||||
# stay close to sage upstream. I didn't open an upstream ticket about it
|
||||
# because the matplotlib update also requires a new dependency (kiwisolver)
|
||||
# and I don't want to invest the time to learn how to add it.
|
||||
./patches/matplotlib-normed-deprecated.patch
|
||||
|
||||
# Update to 20171219 broke the doctests because of insignificant precision
|
||||
# changes, make the doctests less fragile.
|
||||
# I didn't open an upstream ticket because its not entirely clear if
|
||||
# 20171219 is really "released" yet. It is listed on the github releases
|
||||
# page, but not marked as "latest release" and the homepage still links to
|
||||
# the last version.
|
||||
./patches/eclib-regulator-precision.patch
|
||||
|
||||
# sphinx 1.6 -> 1.7 upgrade
|
||||
# https://trac.sagemath.org/ticket/24935
|
||||
./patches/sphinx-1.7.patch
|
||||
|
||||
# https://trac.sagemath.org/ticket/25320
|
||||
(fetchpatch {
|
||||
name = "zero_division_error_formatting.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch/?h=f79070ddd09fa0ad6b340b097bd8d690a7aa35f0";
|
||||
sha256 = "02wsc3wbp8g8dk5jcjyv18d9v537h3zp5v8lwir46j4na4kj0dlb";
|
||||
})
|
||||
|
||||
# Adapt hashes to new boost version
|
||||
# https://trac.sagemath.org/ticket/22243
|
||||
# (this ticket doesn't only upgrade boost but also avoids this problem in the future)
|
||||
(fetchpatch {
|
||||
name = "boost-upgrade.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch?id=a24a9c6b30b93957333a3116196214a931325b69";
|
||||
sha256 = "0z3870g2ms2a81vnw08dc2i4k7jr62w8fggvcdwaavgd1wvdxwfl";
|
||||
})
|
||||
|
||||
# gfan 0.6.2
|
||||
# https://trac.sagemath.org/ticket/23353
|
||||
(fetchpatch {
|
||||
name = "gfan-update.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch/?h=420215fc469cde733ec7a339e59b78ad6eec804c&id=112498a293ea2bf563e41aed35f1aa608f01b349";
|
||||
sha256 = "0ga3hkx8cr23dpc919lgvpi5lmy0d728jkq9z6kf0fl9s8g31mxb";
|
||||
})
|
||||
|
||||
# New glpk version has new warnings, filter those out until upstream sage has found a solution
|
||||
# https://trac.sagemath.org/ticket/24824
|
||||
(fetchpatch {
|
||||
url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/dt-version-glpk-4.65-ignore-warnings.patch";
|
||||
sha256 = "0b9293v73wb4x13wv5zwyjgclc01zn16msccfzzi6znswklgvddp";
|
||||
stripLen = 1;
|
||||
})
|
||||
|
||||
# https://trac.sagemath.org/ticket/25329
|
||||
(fetchpatch {
|
||||
name = "dont-check-exact-glpk-version.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=89d068d8d77316bfffa6bf8e9ebf70b3b3b88e5c";
|
||||
sha256 = "00knwxs6fmymfgfl0q5kcavmxm9sf90a4r76y35n5s55gj8pl918";
|
||||
})
|
||||
|
||||
# https://trac.sagemath.org/ticket/25355
|
||||
(fetchpatch {
|
||||
name = "maxima-5.41.0.patch";
|
||||
url = "https://git.sagemath.org/sage.git/patch/?id=87328023c4739abdf24108038201e3fa9bdfc739";
|
||||
sha256 = "0hxi7qr5mfx1bc32r8j7iba4gzd7c6v63asylyf5cbyp86azpb7i";
|
||||
})
|
||||
|
||||
# Update cddlib from 0.94g to 0.94h.
|
||||
# https://trac.sagemath.org/ticket/25341 (doesn't apply to 8.2 sources)
|
||||
(fetchpatch {
|
||||
url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/u2-version-cddlib-094h.patch";
|
||||
sha256 = "0fmw7pzbaxs2dshky6iw9pr8i23p9ih2y2lw661qypdrxh5xw03k";
|
||||
stripLen = 1;
|
||||
})
|
||||
./patches/revert-269c1e1551285.patch
|
||||
|
||||
|
||||
# Only formatting changes.
|
||||
# https://trac.sagemath.org/ticket/25260
|
||||
./patches/numpy-1.14.3.patch
|
||||
|
||||
# https://trac.sagemath.org/ticket/24374
|
||||
(fetchpatch {
|
||||
name = "networkx-2.1.patch";
|
||||
url = "https://salsa.debian.org/science-team/sagemath/raw/487df9ae48ca1d93d9b1cb3af8745d31e30fb741/debian/patches/u0-version-networkx-2.1.patch";
|
||||
sha256 = "1xxxawygbgxgvlv7b4w8hhzgdnva4rhmgdxaiaa3pwdwln0yc750";
|
||||
stripLen = 1;
|
||||
})
|
||||
|
||||
];
|
||||
|
||||
patches = nixPatches ++ packageUpgradePatches;
|
||||
|
||||
postPatch = ''
|
||||
# make sure shebangs etc are fixed, but sage-python23 still works
|
||||
find . -type f -exec sed \
|
||||
-e 's/sage-python23/python/g' \
|
||||
-i {} \;
|
||||
|
||||
echo '#!${stdenv.shell}
|
||||
python "$@"' > build/bin/sage-python23
|
||||
|
||||
# Do not use sage-env-config (generated by ./configure).
|
||||
# Instead variables are set manually.
|
||||
echo '# do nothing' > src/bin/sage-env-config
|
||||
'';
|
||||
|
||||
configurePhase = "# do nothing";
|
||||
|
||||
buildPhase = "# do nothing";
|
||||
|
||||
installPhase = ''
|
||||
cp -r . "$out"
|
||||
'';
|
||||
}
|
||||
129
pkgs/applications/science/math/sage/sage-with-env.nix
Normal file
129
pkgs/applications/science/math/sage/sage-with-env.nix
Normal file
|
|
@ -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"
|
||||
'';
|
||||
}
|
||||
41
pkgs/applications/science/math/sage/sage-wrapper.nix
Normal file
41
pkgs/applications/science/math/sage/sage-wrapper.nix
Normal file
|
|
@ -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 ];
|
||||
};
|
||||
}
|
||||
32
pkgs/applications/science/math/sage/sage.nix
Normal file
32
pkgs/applications/science/math/sage/sage.nix
Normal file
|
|
@ -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 "$NIX_BUILD_CORES" --optional=sage --long --all
|
||||
'';
|
||||
}
|
||||
97
pkgs/applications/science/math/sage/sagedoc.nix
Normal file
97
pkgs/applications/science/math/sage/sagedoc.nix
Normal file
|
|
@ -0,0 +1,97 @@
|
|||
{ pkgs
|
||||
, stdenv
|
||||
, sage-src
|
||||
, env-locations
|
||||
, sage-with-env
|
||||
, sagelib
|
||||
, python2
|
||||
, psutil
|
||||
, future
|
||||
, sphinx
|
||||
, sagenb
|
||||
, maxima-ecl
|
||||
, networkx
|
||||
, scipy
|
||||
, sympy
|
||||
, matplotlib
|
||||
, pillow
|
||||
, ipykernel
|
||||
, jupyter_client
|
||||
, tachyon
|
||||
, jmol
|
||||
, ipywidgets
|
||||
, typing
|
||||
, cddlib
|
||||
, pybrial
|
||||
}:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
version = sage-src.version;
|
||||
name = "sagedoc-${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
|
||||
'';
|
||||
}
|
||||
139
pkgs/applications/science/math/sage/sagelib.nix
Normal file
139
pkgs/applications/science/math/sage/sagelib.nix
Normal file
|
|
@ -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"
|
||||
'';
|
||||
}
|
||||
49
pkgs/applications/science/math/sage/sagenb.nix
Normal file
49
pkgs/applications/science/math/sage/sagenb.nix
Normal file
|
|
@ -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/${python.sitePackages}/mathjax"
|
||||
'';
|
||||
}
|
||||
|
|
@ -1,36 +0,0 @@
|
|||
diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg
|
||||
index 83e61a7e0d..942ba206c7 100755
|
||||
--- a/build/bin/sage-spkg
|
||||
+++ b/build/bin/sage-spkg
|
||||
@@ -648,8 +648,12 @@ if ! sage-apply-patches; then
|
||||
error_msg "Error applying patches"
|
||||
exit 1
|
||||
fi
|
||||
+
|
||||
+@bash@/bin/bash @patchSageShebangs@ .
|
||||
+
|
||||
cd ..
|
||||
|
||||
+
|
||||
##################################################################
|
||||
# The package has been extracted, prepare for installation
|
||||
##################################################################
|
||||
@@ -671,7 +675,7 @@ write_script_wrapper() {
|
||||
local tmpscript="$(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
|
||||
|
|
@ -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";
|
||||
|
|
@ -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
|
||||
|
|
@ -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 $PYTHON_CONFIGURE"
|
||||
|
||||
|
|
@ -1,18 +0,0 @@
|
|||
diff --git a/build/pkgs/singular/spkg-install b/build/pkgs/singular/spkg-install
|
||||
index 8caafb1699..3c34e6608a 100644
|
||||
--- a/build/pkgs/singular/spkg-install
|
||||
+++ b/build/pkgs/singular/spkg-install
|
||||
@@ -2,6 +2,13 @@
|
||||
## Singular
|
||||
###########################################
|
||||
|
||||
+# Fix hardcoded paths, while making sure to only update timestamps of actually
|
||||
+# changed files (otherwise confuses make)
|
||||
+grep -rlF '/bin/rm' . | while read file
|
||||
+do
|
||||
+ sed -e 's@/bin/rm@rm@g' -i "$file"
|
||||
+done
|
||||
+
|
||||
if [ -z "$SAGE_LOCAL" ]; then
|
||||
echo >&2 "Error: SAGE_LOCAL undefined -- exiting..."
|
||||
echo >&2 "Maybe run 'sage -sh'?"
|
||||
|
|
@ -20381,7 +20381,10 @@ 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 {};
|
||||
|
|
|
|||
Loading…
Reference in a new issue