dev/nixpkgs
1
0
Fork 0
Code Issues Pull Requests Actions 2 Packages Projects Releases Wiki Activity

Merge pull request #216048 from collares/sage-9.8

Browse Source 
sage: 9.7 -> 9.8
This commit is contained in:
Mauricio Collares 2023-02-12 21:48:31 +01:00 committed by GitHub
commit 7e3ba6cec3
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
8 changed files with 32 additions and 146 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
pkgs/applications/science/math/gap/default.nix
View File

@ -134,8 +134,6 @@ stdenv.mkDerivation rec {
# https://github.com/NixOS/nixpkgs/pull/192548#discussion_r992824942
rm -r "$out/share/gap/pkg"
cp -ar pkg tst "$out/share/gap"
makeWrapper "$out/lib/gap/gap" "$out/bin/gap" --add-flags "-l $out/share/gap"
'';
preFixup = ''

10
pkgs/applications/science/math/pari/default.nix
View File

@ -1,6 +1,7 @@
{ lib
, stdenv
, fetchurl
, fetchpatch
, gmp
, libX11
, libpthreadstubs
@ -25,6 +26,15 @@ stdenv.mkDerivation rec {
hash = "sha256-sEYoER7iKHZRmksc2vsy/rqjTq+iT56B9Y+NBX++4N0=";
};
patches = [
# https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2441
(fetchpatch {
name = "fix-find_isogenous_from_Atkin.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pari/patches/bug2441.patch?id=9.8.rc0";
hash = "sha256-DvOUFlFDnopN+MJY6GYRPNabuoHPFch/nNn+49ygznc=";
})
];
buildInputs = [
gmp
libX11

40
pkgs/applications/science/math/sage/README.md
View File

@ -10,7 +10,7 @@ First you should find out which change to nixpkgs is at fault (if you don't alre
If the build broke as a result of a package update, try those solutions in order:
- search the [sage trac](https://trac.sagemath.org/) for keywords like "Upgrade <package>". Maybe somebody has already proposed a patch that fixes the issue. You can then add a `fetchpatch` to `sage-src.nix`.
- search the [sage GitHub repo](https://github.com/sagemath/sage) 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`.
- 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).
@ -19,7 +19,7 @@ If the build broke as a result of a package update, try those solutions in order
```
[user@localhost ~]$ git clone https://github.com/sagemath/sage.git
[user@localhost ~]$ cd sage
[user@localhost sage]$ git checkout 8.2 # substitute the relevant version here
[user@localhost sage]$ git checkout 9.8 # substitute the relevant version here
```
Then make the needed changes and generate a patch with `git diff`:
@ -29,42 +29,10 @@ Then make the needed changes and generate a patch with `git diff`:
[user@localhost ~]$ git diff -u > /path/to/nixpkgs/pkgs/applications/science/math/sage/patches/name-of-patch.patch
```
Now just add the patch to `sage-src.nix` and test your changes. If they fix the problem, [propose them upstream](#proposing-a-sage-patch) and add a link to the trac ticket.
Now just add the patch to `sage-src.nix` and test your changes. If they fix the problem, submit a PR upstream (refer to sages [Developer's Guide](http://doc.sagemath.org/html/en/developer/index.html) for further details).
- pin the package version in `default.nix` and add a note that explains why that is necessary.
## Proposing a sage patch
You can [login the sage trac using GitHub](https://trac.sagemath.org/login). Your username will then be `gh-<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.
Here's the gist, assuming you want to use ssh key authentication. First, [add your public ssh key](https://trac.sagemath.org/prefs/sshkeys). Then:
```
[user@localhost ~]$ git clone https://github.com/sagemath/sage.git
[user@localhost ~]$ cd sage
[user@localhost sage]$ git remote add trac git@trac.sagemath.org:sage.git -t master
[user@localhost sage]$ git checkout -b u/gh-<your-github-username>/<your-branch-name> develop
[user@localhost sage]$ <make changes>
[user@localhost sage]$ git add .
[user@localhost sage]$ git commit
[user@localhost sage]$ git show # review your changes
[user@localhost sage]$ git push --set-upstream trac u/gh-<your-github-username>/<your-branch-name>
```
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).
Now you can [create a new trac ticket](https://trac.sagemath.org/newticket).
- Write a description of the change
- set the type and component as appropriate
- write your real name in the "Authors" field
- write `u/gh-<your-github-username>/<your-branch-name>` in the "Branch" field
- click "Create ticket"
- click "Modify" on the top right of your ticket (for some reason you can only change the ticket status after you have created it)
- set the ticket status from `new` to `needs_review`
- click "Save changes"
Refer to sages [Developer's Guide](http://doc.sagemath.org/html/en/developer/index.html) for further details.
## I want to update sage
You'll need to change the `version` field in `sage-src.nix`. Afterwards just try to build and let nix tell you which patches no longer apply (hopefully because they were adopted upstream). Remove those.
@ -74,5 +42,5 @@ If the problem is not obvious, you can try to first update sage to an intermedia
## Well, that didn't help!
If you couldn't fix the problem, create a GitHub issue on the nixpkgs repo and ping @timokau (or whoever is listed in the `maintainers` list of the sage package).
If you couldn't fix the problem, create a GitHub issue on the nixpkgs repo and ping the sage maintainers (as listed in the sage package).
Describe what you did and why it didn't work. Afterwards it would be great if you help the next guy out and improve this documentation!

3
pkgs/applications/science/math/sage/env-locations.nix
View File

@ -35,7 +35,8 @@ writeTextFile rec {
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}/share/gap'
export GAP_LIB_DIR='${gap}/lib/gap'
export GAP_SHARE_DIR='${gap}/share/gap'
export ECLDIR='${maxima.lisp-compiler}/lib/${maxima.lisp-compiler.pname}-${maxima.lisp-compiler.version}/'
export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs"
export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona"

26
pkgs/applications/science/math/sage/patches/pari-2.15.1-upgrade-rebased.patch
View File

@ -1,26 +0,0 @@
diff --git a/src/sage/geometry/polyhedron/backend_normaliz.py b/src/sage/geometry/polyhedron/backend_normaliz.py
index 86b89632a5..ca8a43b248 100644
--- a/src/sage/geometry/polyhedron/backend_normaliz.py
+++ b/src/sage/geometry/polyhedron/backend_normaliz.py
@@ -53,7 +53,7 @@ def _number_field_elements_from_algebraics_list_of_lists_of_lists(listss, **kwds
1.732050807568878?
sage: from sage.geometry.polyhedron.backend_normaliz import _number_field_elements_from_algebraics_list_of_lists_of_lists
sage: K, results, hom = _number_field_elements_from_algebraics_list_of_lists_of_lists([[[rt2], [1]], [[rt3]], [[1], []]]); results # optional - sage.rings.number_field
- [[[-a^3 + 3*a], [1]], [[-a^2 + 2]], [[1], []]]
+ [[[-a^3 + 3*a], [1]], [[a^2 - 2]], [[1], []]]
"""
from sage.rings.qqbar import number_field_elements_from_algebraics
numbers = []
diff --git a/src/sage/lfunctions/pari.py b/src/sage/lfunctions/pari.py
index d2b20f1891..6c31efe239 100644
--- a/src/sage/lfunctions/pari.py
+++ b/src/sage/lfunctions/pari.py
@@ -339,7 +339,7 @@ def lfun_eta_quotient(scalings, exponents):
0.0374412812685155
sage: lfun_eta_quotient([6],[4])
- [[Vecsmall([7]), [Vecsmall([6]), Vecsmall([4])]], 0, [0, 1], 2, 36, 1]
+ [[Vecsmall([7]), [Vecsmall([6]), Vecsmall([4]), 0]], 0, [0, 1], 2, 36, 1]
sage: lfun_eta_quotient([2,1,4], [5,-2,-2])
Traceback (most recent call last):

74
pkgs/applications/science/math/sage/sage-src.nix
View File

@ -57,14 +57,14 @@ let
);
in
stdenv.mkDerivation rec {
version = "9.7";
version = "9.8";
pname = "sage-src";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
sha256 = "sha256-MYpCp18wqKwCa+tcJ7He14p1FXDlVm1vubQqQS9g3LY=";
sha256 = "sha256-dDbrzJXsOBARYfJz0r7n3LbaoXHnx7Acz6HBa95NV9o=";
};
# Patches needed because of particularities of nix or the way this is packaged.
@ -89,14 +89,6 @@ stdenv.mkDerivation rec {
# To help debug the transient error in
# https://trac.sagemath.org/ticket/23087 when it next occurs.
./patches/configurationpy-error-verbose.patch
# https://trac.sagemath.org/ticket/33907
(fetchSageDiff {
name = "interfaces-expectpy-intermittent.patch";
base = "9.8.beta6";
rev = "6f5c1c2fc8bcfb5e6555716d05ce70511795ffa1";
sha256 = "sha256-z8FQxtrk62MHzPjrUTad+fMAE6XV8GTsLWKgGOM3zBg=";
})
];
# Patches needed because of package updates. We could just pin the versions of
@ -119,28 +111,12 @@ stdenv.mkDerivation rec {
# adapted from https://trac.sagemath.org/ticket/23712#comment:22
./patches/tachyon-renamed-focallength.patch
# https://trac.sagemath.org/ticket/34118
(fetchSageDiff {
name = "sympy-1.11-upgrade.patch";
base = "9.7";
rev = "52815744bde2b682245b6f985a112f7cb8666056";
sha256 = "sha256-gv6z6JkQ6S6oCJQNkVgcPVvzlplyvR1nC7pWmcUiSc0=";
})
# https://trac.sagemath.org/ticket/34460
(fetchSageDiff {
name = "ipywidgets-8-upgrade.patch";
base = "9.7";
rev = "2816dbacb342398a23bb3099e20c92c8020ab0fa";
sha256 = "sha256-tCOsMxXwPkRg3FJGVvTqDzlWdra78UfDY6nci0Nr9GI=";
})
# https://trac.sagemath.org/ticket/34391
(fetchSageDiff {
name = "gap-4.12-upgrade.patch";
base = "9.8.beta2";
rev = "eb8cd42feb58963adba67599bf6e311e03424328";
sha256 = "sha256-0dKewOZe2n3PqSdxCJt18FkqwTdrD0VA5MXAMiTW8Tw=";
base = "9.8.beta7";
rev = "dd4a17281adcda74e11f998ef519b6bd0dafb043";
sha256 = "sha256-UQT9DO9xd5hh5RucvUkIm+rggPKu8bc1YaSI6LVYH98=";
})
# https://trac.sagemath.org/ticket/34701
@ -151,46 +127,6 @@ stdenv.mkDerivation rec {
sha256 = "sha256-9BhQLFB3wUhiXRQsK9L+I62lSjvTfrqMNi7QUIQvH4U=";
})
# https://trac.sagemath.org/ticket/34537
(fetchSageDiff {
name = "pari-2.15.1-upgrade.patch";
squashed = true;
base = "54cd6fe6de52aee5a433e0569e8c370618cb2047"; # 9.8.beta1
rev = "1e86aa26790d84bf066eca67f98a60a8aa3d4d3a";
sha256 = "sha256-LUgcMqrKXWb72Kxl0n6MV5unLXlQSeG8ncN41F7TRSc=";
excludes = ["build/*"
"src/sage/geometry/polyhedron/base_number_field.py"
"src/sage/geometry/polyhedron/backend_normaliz.py"
"src/sage/lfunctions/pari.py"];
})
# Some files were excluded from the above patch due to
# conflicts. The patch below contains rebased versions.
./patches/pari-2.15.1-upgrade-rebased.patch
# https://trac.sagemath.org/ticket/34668
(fetchSageDiff {
name = "matplotlib-3.6-upgrade.patch";
base = "9.8.beta2";
rev = "5501e0de0dca1cff0355326dd42bd8c7e5749568";
sha256 = "sha256-ceJkVaecIsZewN8v/3gPQXFbFjv5Akz6zEFg/ToXdek=";
})
# https://trac.sagemath.org/ticket/34693
(fetchSageDiff {
name = "matplotlib-3.6-docbuilding.patch";
base = "9.8.beta4";
rev = "64589686c261d33e6b5aff2589bcae8af004bcc6";
sha256 = "sha256-j5AMY1TmhP+HBBBYaFZSkABJ5vtwe6iP2LRfGEgSm8Q=";
})
# https://trac.sagemath.org/ticket/34615
(fetchSageDiff {
name = "sphinx-5.2-upgrade.patch";
base = "9.8.beta1";
rev = "8f8af65e54d3a9962cfab40f15dc23f4e955b43f";
sha256 = "sha256-yhDdyxnXSSkqLcuOPBWSEBc26rk1Od3gLcWW8S2p8bY=";
})
# temporarily paper over https://github.com/jupyter-widgets/ipywidgets/issues/3669
./patches/ipywidgets-on_submit-deprecationwarning.patch

10
pkgs/development/libraries/science/math/sympow/default.nix
View File

@ -1,5 +1,6 @@
{ lib, stdenv
, fetchFromGitLab
, fetchpatch
, makeWrapper
, which
, autoconf
@ -20,7 +21,14 @@ stdenv.mkDerivation rec {
sha256 = "132l0xv00ld1svvv9wh99wfra4zzjv2885h2sq0dsl98wiyvi5zl";
};
patches = [ ./clean-extra-logfile-output-from-pari.patch ];
patches = [
./clean-extra-logfile-output-from-pari.patch
(fetchpatch {
name = "null-terminate-dupdirname.patch";
url = "https://gitlab.com/rezozer/forks/sympow/-/merge_requests/5.diff";
sha256 = "sha256-yKjio+qN9teL8L+mb7WOBN/iv545vRIxW20FJU37oO4=";
})
];
postUnpack = ''
patchShebangs .

13
pkgs/development/python-modules/fpylll/default.nix
View File

@ -1,7 +1,6 @@
{ stdenv
, lib
, fetchFromGitHub
, fetchpatch
, buildPythonPackage
, pkgconfig
, gmp
@ -16,23 +15,15 @@
buildPythonPackage rec {
pname = "fpylll";
version = "0.5.7";
version = "0.5.9";
src = fetchFromGitHub {
owner = "fplll";
repo = "fpylll";
rev = version;
sha256 = "sha256-iUPreJ8BSB8LDisbJis0xn8ld6+Nf9Z4AP8SWJlCfZg=";
sha256 = "sha256-T6l6hKzRDevlLyLu5H+bnEdl0OhsPer1coCDiftbPAk=";
};
patches = [
(fetchpatch {
name = "remove-strategies-doctest.patch";
url = "https://github.com/fplll/fpylll/commit/3edffcd189e9d827a322d83b0f84d32e5f067442.patch";
sha256 = "sha256-U7qOIbVzUNwYmjOPryjnE3J+MX/vMwm3T0UyOZ5ylLc=";
})
];
buildInputs = [
gmp
pari