118 lines
7.2 KiB
Markdown
118 lines
7.2 KiB
Markdown
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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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